[galaxy-dev] August 11, 2014 Galaxy Distribution

[Jennifer Jackson]

August 11, 2014 Galaxy Distribution 




/
/
_Complete News Brief 
___


/Highlights:///

.Security alert from July 31st, upgrade now
.Citations 
: 
DOIs, bibtex, and much much more
. Docker : You voted, 
we've/got it/, with a little help from our friends (you!)

. Significant Workflow, API, Job, Tool Shed, and Dataset management updates
. Fixes, tunings, plus just a drop of ? Gossip




*getgalaxy.org *

*galaxy-dist.readthedocs.org *



*bitbucket.org/galaxy/galaxy-dist *



*new*:



$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

*upgrade*:



$ hg pull
$ hg update latest_2014.08.11


/Thanks for using Galaxy!/

The Galaxy Team 






___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] August 11, 2014 Galaxy Distribution

[Jennifer Jackson]

August 11, 2014 Galaxy Distribution 




/
/
_Complete News Brief 
___


/Highlights:///

.Security alert from July 31st, upgrade now
.Citations 
: 
DOIs, bibtex, and much much more
. Docker, docker,DOCKER 
. You voted, we've/got 
it/, with a little help from our friends (you!)

. Significant Workflow, API, Job, Tool Shed, and Dataset management updates
. Fixes, tunings, plus just a drop of ? Gossip




*getgalaxy.org *

*galaxy-dist.readthedocs.org *



*bitbucket.org/galaxy/galaxy-dist *



*new*:



$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

*upgrade*:



$ hg pull
$ hg update latest_2014.06.02


/Thanks for using Galaxy!/

The Galaxy Team 




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] sorting of files in data libraries

[Jennifer Jackson]

Hi Sarah,

Data libraries are in an active enhancement phase. There are many 
changes recent, in progress, and planned that you can review in Trello.


This is one of them, and the specific card is here: 
https://trello.com/c/0RnzM6lP


For now, uploading with the name you wish to use in the UI is how to 
achieve the desired sort.


Thanks!

Jen
Galaxy team

On 5/23/14 2:37 AM, Sarah Diehl wrote:

Hi everyone,

I uploaded a bunch of files to the Galaxy data libraries with the option "Upload files from 
filesystem paths" and "Link to files without copying to Galaxy". Afterwards I edited 
the names that are displayed in Galaxy. However, now the files are not alphabetically sorted 
anymore. I tried moving them around, but the order stayed the same. Is this on purpose and is there 
a way to change it?

Thanks,
Sarah
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Join Paired-End reads (version 1.0.3)

[Jennifer Jackson]

Hello Julien,

I don't know if you have had help already or not, but contacting the 
owners of this instance is the probably the quickest path to an answer 
(and possibly shared code). At this instance, under "Help -> Support", 
they have modified the link to point to the email address for their 
team. I'd start there.


Take care,

Jen
Galaxy team

On 5/28/14 7:38 AM, Julien Daligault wrote:

Hello,

I am interested by a wrapper in the galaxy-dev.jgi-psf.org : Join 
Paired-End reads (version 1.0.3) 
(https://galaxy-dev.jgi-psf.org/tool_runner?tool_id=jgi_rnd_merge_pe)
I didn't find it in the tool shed, where is it possible to access to 
this wrapper ?


Regards,

Julien



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] SAM/BAM To Counts dataset generation errors

[Jennifer Jackson]

Hello,

This question and this Biostar post are the same question, correct?
https://biostar.usegalaxy.org/p/7979/

Glad this is resolved. Next time, would be best to post to just one place.

Thanks!
Jen
Galaxy team

On 6/10/14 3:55 AM, Israel Bravo wrote:


When trying SAM/BAM to Counts I get the following error message:   
pysam not installed; please install it


But a) pysam was not in this tool dependencies;
   b) pysam/0.7.7 is already installe



--
Israel Bravo on about.me

Israel Bravo
about.me/bravobih




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] June 2, 2014 Galaxy Distribution

[Jennifer Jackson]

June 2, 2014 Galaxy Distribution 



*News Brief 
**Highlights:*


 * Dataset Collections introduced
 * Changes to database build (dbkey) organization
 * Enhancements to Tool configuration and Workflow options
 * Trackster, User Interface, and Admin panel upgrades
 * Significant updates to Admin and Job functionality
 * Tool Shed repository and API additions
 * Data updates plus new Security features and Bug fixes

*
new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

*upgrade*: $ hg pull
$ hg update latest_2014.06.02


getgalaxy.org 
galaxy-dist.readthedocs.org 
bitbucket.org/galaxy/galaxy-dist *
*


/Thanks for using Galaxy!/

The Galaxy Team 


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Uploading big data in local installation of galaxy

[Jennifer Jackson]

Hi Amit,

You may have solved this already, but if not, there are (at least) two 
good options, with the second better if your data is already on the same 
computer that you have Galaxy running. A file 2G or over will never load 
through the browser - this same rule applies to a local and the public 
Main site (and anywhere else that I am aware of).


Start by setting with a basic 'production' configuration
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

1 - Enable FTP as described in the link above

2 - Load the data into a library through one of these options
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

I am going to post this to the galaxy-dev list to help others that may 
have the same question. Next time, for the speediest reply, post 
directly here with local admin questions. You'll benefit from replies 
from our team and the community (super helpful!).


Best,

Jen
Galaxy team


Dear Jennifer,

I installed galaxy locally on my linux machine including the tool 
shed, but the file upload keeps
showing the "uploading" status forever for big datasets ( for example 
CAGE reads > 6GB).


Could you please help in sorting out the problem ?

warm regards,
Amit.


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] permanently deleting histories

[Jennifer Jackson]

Hi Jennifer,

Active and Deleted histories can be permanently deleted using from the 
History pane "Options -> Saved Histories", then at the top of the middle 
panel click on "Advanced Search", then click on "status: all". Check the 
box for the histories to be discarded and then click on the button 
"Permanently delete".


Full instructions with a video walk-through are here:
https://wiki.galaxyproject.org/Learn/ManagingDatasets#Delete_vs_Delete_Permanently

Best,

Jen
Galaxy team

On 5/5/14 10:33 AM, Jennifer Gotenstein wrote:
I need to clear space from my quota of usage in my galaxy main user 
account, but I deleted 2 histories, rather than permanently deleting 
them. How can I access them again so that I may permanently delete 
them to clear the space?


Thank you,

Jennifer


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Portability and versionig in Galaxy

[Jennifer Jackson]

Hi Sally,

I can point you to a few resources that explain what we are working on, 
what we plan to work on, and how the architecture is put together. All 
possible development directions versus what is prioritized because it 
fits the larger project goals will be hopefully be clearer after a 
review. Galaxy development is highly collaborative and we do our best to 
be transparent. Anyone can freely publish work within our framework to 
share with others also using Galaxy (tools in the Tool Shed, 
data/analysis/workflows/etc. on the public server).


Looks for changes across time for workflows in releases here:
https://wiki.galaxyproject.org/DevNewsBriefs

Read our publications about architecture here:
https://wiki.galaxyproject.org/CitingGalaxy

Trello cards for ideas, in-progress, recently completed work (all areas):
https://wiki.galaxyproject.org/Issues

Code documentation:
http://galaxy-dist.readthedocs.org/en/latest/

Take care,

Jen
Galaxy team

On 4/30/14 2:29 PM, Golestan (Sally) Radwan wrote:

Hi All,

I am completely new to galaxy but part of my PhD research is to look 
at portability issues of workloads across different versions. I've 
tried looking at the wiki and the various pieces of documentation but 
no luck so far. Can someone please point me to a document or tutorial 
that explains how this is currently done in Galaxy and also any 
issues/gaps that may be worth addressing?


I am also generally interested in how Galaxy works "under the hood". 
Is there a document that explains the architecture and design?


Many thanks in advance!

Sally.


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Cannot access saved history nor saved datasets

[Jennifer Jackson]

Hi Joshua,

If you are still having issues, you'll want to contact the folks running 
that specific instance for support. They'll know the state of the 
server. See this link, under the section "User Support" for their google 
group contact:

https://wiki.galaxyproject.org/PublicGalaxyServers#Cistrome_Analysis_Pipeline

Best,

Jen
Galaxy team

On 5/1/14 12:01 PM, Joshua David Aaker wrote:
I am able to use my current history and run tools but I can't move 
away nor create new histories.


I am currently using the Cistrome instance of Galaxy.

Here is the error I receive:


  Internal Server Error


Galaxy was unable to successfully complete your request

URL: http://cistrome.org/ap/history/list
Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>> app_iter *=* 
self*.*application*(*environ*,* sr_checker*)*|

Module paste.recursive:*84* in |__call__|
|>> *return* 
self*.*application*(*environ*,* start_response*)*|

Module paste.httpexceptions:*633* in |__call__|
|>> *return* 
self*.*application*(*environ*,* start_response*)*|

Module galaxy.web.framework.base:*132* in |__call__|
|>> *return* 
self*.*handle_request*(* environ*,* start_response *)*|

Module galaxy.web.framework.base:*190* in |handle_request|
|>> body *=* method*(* trans*,* 
kwargs *)*|

Module galaxy.web.framework:*98* in |decorator|
|>> *return* func*(* self*,* 
trans*,* ***args*,* kwargs *)*|

Module galaxy.webapps.galaxy.controllers.history:*294* in |list|
|>> *return* 
self*.*stored_list_grid*(* trans*,* status*=*status*,* 
message*=*message*,* kwargs *)*|

Module galaxy.web.framework.helpers.grids:*209* in |__call__|
|>> total_num_rows *=* 
query*.*count*(**)*|

Module sqlalchemy.orm.query:*2571* in |count|
Module sqlalchemy.orm.query:*2215* in |scalar|
Module sqlalchemy.orm.query:*2184* in |one|
Module sqlalchemy.orm.query:*2227* in |__iter__|
Module sqlalchemy.orm.query:*2242* in |_execute_and_instances|
Module sqlalchemy.engine.base:*1449* in |execute|
Module sqlalchemy.engine.base:*1584* in |_execute_clauseelement|
Module sqlalchemy.engine.base:*1698* in |_execute_context|
Module sqlalchemy.engine.base:*1691* in |_execute_context|
Module sqlalchemy.engine.default:*331* in |do_execute|
Module MySQLdb.cursors:*173* in |execute|
Module MySQLdb.connections:*36* in |defaulterrorhandler|
*OperationalError: (OperationalError) (1030, 'Got error 28 from 
storage engine') 'SELECT count(*) AS count_1 \nFROM (SELECT history.id 
AS history_id, history.create_time AS history_create_time, 
history.update_time AS history_update_time, history.user_id AS 
history_user_id, history.name AS history_name, history.hid_counter AS 
history_hid_counter, history.deleted AS history_deleted, 
history.purged AS history_purged, history.importing AS 
history_importing, history.genome_build AS history_genome_build, 
history.importable AS history_importable, history.slug AS 
history_slug, history.published AS history_published \nFROM history 
\nWHERE history.importing = %s AND %s = history.user_id AND 
history.deleted = %s ORDER BY history.update_time DESC) AS anon_1' (0, 
1889L, 0)*


Any suggestions or more information you need?

-Josh


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

[Jennifer Jackson]

g 15 11:20:55 2013 -0400
summary: Branch close

changeset:   10364:e68eee8054d2
branch:  sort
parent:  10362:1d91e253734e
user:Dannon Baker 
date:Wed Aug 07 13:36:25 2013 -0400
summary: Branch close

changeset:   10346:a849924d6f9d
branch:  extended_metadata
parent:  10343:30f0aeacf88a
user:Dannon Baker 
date:Tue Aug 06 15:58:00 2013 -0400
summary: Close extended_metadata branch

changeset:   10132:10810850afaa
branch:  list_published_export
parent:  10129:1d71126419b2
user:jeremy goecks 
date:Fri Jun 21 09:27:35 2013 -0400
summary: Close list_published_export branch

changeset:   10119:6090712e7f29
branch:  provenance
parent:  10115:471457199db2
user:Dannon Baker 
date:Thu Jun 20 12:58:16 2013 -0400
summary: Close provenance branch

changeset:   10114:49771dac79f2
branch:  provenance
parent:  10108:0bb601dceb65
user:Dannon Baker 
date:Thu Jun 20 11:02:00 2013 -0400
summary: Close provenance branch

changeset:   10091:fce9396b9a81
branch:  search
parent:  10089:fd3a82d33bb6
user:Dannon Baker 
date:Tue Jun 18 17:22:52 2013 -0400
summary: Close search branch

changeset:   9403:97776a49c3ed
branch:  catless-file-merge
parent:  9399:510b063792de
user:Daniel Blankenberg 
date:Mon Apr 15 13:09:25 2013 -0400
summary: Close catless-file-merge branch.

changeset:   9343:4e08f4804b75
branch:  error-message-fix
parent:  9336:b2a5169daea4
user:Dannon Baker 
date:Tue Apr 09 13:25:03 2013 -0400
summary: Close branch from Bjorn's error-message-fix pull request

changeset:   8838:499ce7fb3821
branch:  bugfixes
parent:  8835:c8b7dfb1e76d
user:Dannon Baker 
date:Wed Feb 13 13:28:47 2013 -0500
summary: Close branch bugfixes from PR#120


Jennifer Jackson a écrit :

Hello Sarah,

This commit was made some time ago and is already in the 
distribution. Are you running the latest distribution?


And you have uncommented the configuration line for this in your 
universe.wgsi.ini file?


# Directory where chrom len files are kept, currently mainly used by 
trackster

#len_file_path = tool-data/shared/ucsc/chrom <--- here

Upgrade and adjust the file as needed.
https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution

I am going to forward this over to the galaxy-...@bx.psu.edu mailing 
list for further troubleshooting, should this not resolve the 
problem. Please keep all replies on that list.


Best,

Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists

*Galaxy Biostar is replacing the galaxy-user mailing list! /Update 
now! /**

**   Here's how ->>> https://wiki.galaxyproject.org/Support/Biostar**
*

On 4/22/14 3:25 AM, Sarah Maman wrote:

Hello,

I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (genome_test.len in 
galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in 
.loc fils in tool-data/) but "Intersect multiple sorted BED files" 
gives this error message :
An error occurred running this job: /Epilog : job finished at lun. 
mars 24 15:55:04 CET 2014
Error: The requested genome file 
(//galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) 
could not be opened. Exiting!


So, /I have integrated the code modification submitted in Galaxy 
Central 
(https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2):

-chrom_info = os.path.join( trans.app.config.tool_data_path, 
'shared','ucsc','chrom', "%s.len" % input_dbkey )
+chrom_info = os.path.join( trans.app.config.len_file_path, 
"%s.len" % input_dbkey )

But I always have the same error message.

Could you please help us ?
Thanks in advance,
Sarah

--
   --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53
  --*--


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org



--
   --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.or

Re: [galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

[Jennifer Jackson]

g 15 11:20:55 2013 -0400
summary: Branch close

changeset:   10364:e68eee8054d2
branch:  sort
parent:  10362:1d91e253734e
user:Dannon Baker 
date:Wed Aug 07 13:36:25 2013 -0400
summary: Branch close

changeset:   10346:a849924d6f9d
branch:  extended_metadata
parent:  10343:30f0aeacf88a
user:Dannon Baker 
date:Tue Aug 06 15:58:00 2013 -0400
summary: Close extended_metadata branch

changeset:   10132:10810850afaa
branch:  list_published_export
parent:  10129:1d71126419b2
user:jeremy goecks 
date:Fri Jun 21 09:27:35 2013 -0400
summary: Close list_published_export branch

changeset:   10119:6090712e7f29
branch:  provenance
parent:  10115:471457199db2
user:Dannon Baker 
date:Thu Jun 20 12:58:16 2013 -0400
summary: Close provenance branch

changeset:   10114:49771dac79f2
branch:  provenance
parent:  10108:0bb601dceb65
user:Dannon Baker 
date:Thu Jun 20 11:02:00 2013 -0400
summary: Close provenance branch

changeset:   10091:fce9396b9a81
branch:  search
parent:  10089:fd3a82d33bb6
user:Dannon Baker 
date:Tue Jun 18 17:22:52 2013 -0400
summary: Close search branch

changeset:   9403:97776a49c3ed
branch:  catless-file-merge
parent:  9399:510b063792de
user:Daniel Blankenberg 
date:Mon Apr 15 13:09:25 2013 -0400
summary: Close catless-file-merge branch.

changeset:   9343:4e08f4804b75
branch:  error-message-fix
parent:  9336:b2a5169daea4
user:Dannon Baker 
date:Tue Apr 09 13:25:03 2013 -0400
summary: Close branch from Bjorn's error-message-fix pull request

changeset:   8838:499ce7fb3821
branch:  bugfixes
parent:  8835:c8b7dfb1e76d
user:Dannon Baker 
date:Wed Feb 13 13:28:47 2013 -0500
summary: Close branch bugfixes from PR#120


Jennifer Jackson a écrit :

Hello Sarah,

This commit was made some time ago and is already in the 
distribution. Are you running the latest distribution?


And you have uncommented the configuration line for this in your 
universe.wgsi.ini file?


# Directory where chrom len files are kept, currently mainly used by 
trackster

#len_file_path = tool-data/shared/ucsc/chrom <--- here

Upgrade and adjust the file as needed.
https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution

I am going to forward this over to the galaxy-...@bx.psu.edu mailing 
list for further troubleshooting, should this not resolve the 
problem. Please keep all replies on that list.


Best,

Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists

*Galaxy Biostar is replacing the galaxy-user mailing list! /Update 
now! /**

**   Here's how ->>> https://wiki.galaxyproject.org/Support/Biostar**
*

On 4/22/14 3:25 AM, Sarah Maman wrote:

Hello,

I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (genome_test.len in 
galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in 
.loc fils in tool-data/) but "Intersect multiple sorted BED files" 
gives this error message :
An error occurred running this job: /Epilog : job finished at lun. 
mars 24 15:55:04 CET 2014
Error: The requested genome file 
(//galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) 
could not be opened. Exiting!


So, /I have integrated the code modification submitted in Galaxy 
Central 
(https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2):

-chrom_info = os.path.join( trans.app.config.tool_data_path, 
'shared','ucsc','chrom', "%s.len" % input_dbkey )
+chrom_info = os.path.join( trans.app.config.len_file_path, 
"%s.len" % input_dbkey )

But I always have the same error message.

Could you please help us ?
Thanks in advance,
Sarah

--
   --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53
  --*--


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org



--
   --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.or

[galaxy-dev] "Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

[Jennifer Jackson]

Hello Sarah,

This commit was made some time ago and is already in the distribution. 
Are you running the latest distribution?


And you have uncommented the configuration line for this in your 
universe.wgsi.ini file?


# Directory where chrom len files are kept, currently mainly used by 
trackster

#len_file_path = tool-data/shared/ucsc/chrom  <--- here

Upgrade and adjust the file as needed.
https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution

I am going to forward this over to the galaxy-...@bx.psu.edu mailing 
list for further troubleshooting, should this not resolve the problem. 
Please keep all replies on that list.


Best,

Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists

*Galaxy Biostar is replacing the galaxy-user mailing list! /Update now! /**
**   Here's how ->>> https://wiki.galaxyproject.org/Support/Biostar**
*

On 4/22/14 3:25 AM, Sarah Maman wrote:

Hello,

I try to use "Intersect multiple sorted BED files" tool without success.
A genome_test have been added in galaxy (genome_test.len in 
galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc 
fils in tool-data/) but "Intersect multiple sorted BED files" gives 
this error message :
An error occurred running this job: /Epilog : job finished at lun. 
mars 24 15:55:04 CET 2014
Error: The requested genome file 
(//galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could 
not be opened. Exiting!


So, /I have integrated the code modification submitted in Galaxy 
Central 
(https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2):

-chrom_info = os.path.join( trans.app.config.tool_data_path, 
'shared','ucsc','chrom', "%s.len" % input_dbkey )
+chrom_info = os.path.join( trans.app.config.len_file_path, 
"%s.len" % input_dbkey )

But I always have the same error message.

Could you please help us ?
Thanks in advance,
Sarah

--
   --*--
Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53
  --*--


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Galaxy - Cloudman

[Jennifer Jackson]

Posting to the galaxy-...@bx.psu.edu mailing list.
https://wiki.galaxyproject.org/MailingLists

My instance of Galaxy seems to be stuck (same place since last night) 
and I have received the error message several times now.


Pasting the error message below:

*Details*

user



username



adeglincer

quota_percent



68

total_disk_usage



184947273683

nice_total_disk_usage



172.2 GB

email



xxx

is_admin



false

tags_used



model_class



User

id



xxx

source



HDACollection(xxx)

xhr



readyState



4

responseText



{"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}

responseJSON



err_msg



Uncaught exception in exposed API method:

err_code



0

status



500

statusText



Internal Server Error

responseHeaders



Date



Thu, 24 Apr 2014 20:51:39 GMT

cache-control



max-age=0,no-cache,no-store

Server



nginx/1.4.7

Connection



keep-alive

Transfer-Encoding



chunked

Content-Type



application/json

options



data



parse



true

emulateHTTP



false

emulateJSON



false


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Announcing the Galaxy Biostar Forum

[Jennifer Jackson]

Dear Galaxy Community,

Galaxy has teamed up with Biostar to create a Galaxy User support forum 
at https://biostar.usegalaxy.org!


We want to create a space where researchers using Galaxy can come 
together and share both scientific advice and practical tool help. 
Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if 
you have something to say about Using Galaxy, this is the place to do it!


Current integration with usegalaxy.org
* We imported the whole history of galaxy-u...@bx.psu.edu mailing list 
into Biostar
* If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy 
Biostar) you will be automatically logged in.
* A Galaxy Biostar account will be created for you if it did not 
previously exist. To obtain this account’s password please use the 
password reset feature of Galaxy Biostar 
(https://biostar.usegalaxy.org/accounts/password/reset/).
* When you have a question, search Biostar directly from any Galaxy tool 
page.


Read more about how to get started at 
https://wiki.galaxyproject.org/Support/Biostar


Roll-out phase
* Galaxy Biostar is available at http://biostar.usegalaxy.org and will 
be our primary avenue for support
* The galaxy-u...@bx.psu.edu mailing list will continue to be supported 
during the transition but starting now please use the 
biostar.usegalaxy.org forum to ask all questions about using Galaxy.
* Please do not double post to both Galaxy Biostar and 
galaxy-u...@bx.psu.edu
* Send us feedback through the forum's post "Welcome to Biostar" to tell 
us what you think.


What’s next
* Notice will be given when the galaxy-u...@bx.psu.edu mailing list is 
retired.

* Archives of galaxy-u...@bx.psu.edu will remain accessible.

We hope you will like the change and look forward to any feedback you 
may have.


Thank you for using Galaxy!
The Galaxy team
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Announcing the Galaxy Biostar Forum

[Jennifer Jackson]

*

Dear Galaxy Community,


Galaxy has teamed up with Biostar to create a Galaxy User support forum 
at https://biostar.usegalaxy.org !



We want to create a space where researchers using Galaxy can come 
together and share both scientific advice and practical tool help. 
 Whether on *usegalaxy.org *, 
a*****Cloudman  
*instance, or any other 
 *Galaxy 
*, if you have something to say about Using 
Galaxy, this is the place to do it!



Current integration with usegalaxy.org

 *

   We imported the whole history of galaxy-u...@bx.psu.edu mailing list
   into Biostar

 *

   If you access Galaxy Biostar from *usegalaxy.org*
    (Top*m*enu: "Help ->Galaxy Biostar")you will
   be automatically logged in. A Galaxy Biostar account will be created
   for you if it did not previously exist. To obtain this account's
   password please use the password reset feature of Galaxy Biostar
   (https://biostar.usegalaxy.org/accounts/password/reset/).

 *

   When you have a question, search Biostar directly from any Galaxy
   tool page.


Read more about how to get startedat 
https://wiki.galaxyproject.org/Support/Biostar



Roll-out phase

 *

   Galaxy Biostar is available at *http://biostar.usegalaxy.org*and
   will be our primary avenue for support

 *

   The galaxy-u...@bx.psu.edu mailing list will continue to be
   supported during the transitionbut starting now please use the
   biostar.usegalaxy.org forumto ask all
   questions about using Galaxy.

 *

   Please do not double postto both Galaxy Biostar and
   galaxy-u...@bx.psu.edu

 *

   Send us feedback through the forum's post *"Welcome to Biostar"* to
   tell us what you think.


What's next

 *

   Notice will be given when the galaxy-u...@bx.psu.edu mailing list is
   retired.

 *

   Archives of galaxy-u...@bx.psu.edu will remain accessible.


We hope you will like the change and look forward to any feedback you 
may have.



Thank you for using Galaxy!


*Galaxy Team *

*

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] registration problem

[Jennifer Jackson]

Hi Wesley, Carlos,

We'd very much appreciate that you both took the time to report details 
about this issue. We captured this in the Trello ticket: 
https://trello.com/c/FLlynVZm


This issue was closed in another thread on 2/4/2014, please see ticket 
for details. May a known already, but just in case Wesley, or others 
finding this thread through a search, didn't see that one, we wanted to 
post follow-up here, too, and a "Big thanks!".


As for documentation, we decided to add this to our wiki for now 
(cookies were unique to this issue). More concerning trouble-shooting in 
the wiki is gaining traction (new page/s) .. community contributions 
welcomed!

https://wiki.galaxyproject.org/Admin/GetGalaxy#Troubleshooting

Best,

Jen

On 3/11/13 6:34 AM, Carlos Borroto wrote:

On Mon, Mar 11, 2013 at 9:04 AM, Wesley Schaal
 wrote:

When trying to register a new user (which will be the administrator), the registration 
page declare success ("Now logged in as foo") but I am still just an anonymous 
user. If I try to login, it appears to succeed but I'm still anonymous. If I purposely 
enter the wrong password, the system complains as it should but I never get proper 
credentials.

I have seen this several time in my local install and is always a
cookie's problem. Please delete all cookies for you galaxy hostname
and try again.

I wonder if the wiki should have a FAQ section and this cookie's issue
should be at the top.

Hope it helps,
Carlos

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] extract_genomic_dna.py

[Jennifer Jackson]

Hi Adhemar,

Very glad this is working out for your own use. I created a ticket to 
include your suggested enhancement globally:

https://trello.com/c/jbhy3dSM

Should you wish to create a ticket in the future, this is how:
https://wiki.galaxyproject.org/Issues

Community contributions are reviewed/incorporated through pull-requests, 
if you would like to submit. No guarantees, but either way this moves it 
along and you'll then know the status:

https://wiki.galaxyproject.org/Develop
 -> See ' Source code and documentation'
https://bitbucket.org/galaxy/galaxy-central/pull-requests

Best,

Jen
Galaxy team

On 3/28/14 5:41 AM, Adhemar wrote:

Hi,
In order to have the transcript_id for each sequence extracted from 
the cuffmerge .gtf file I had to change the extract_genomic_dna.py by 
adding the following lines after line 153:


attributes = gff_util.parse_gff_attributes( feature[8] )
if ( "transcript_id" in attributes ):
 name = attributes.get( "transcript_id", None )


This way the variable name gets the transcript_id if it exists.

If it's correct, I would appreciate this modification in future galaxy 
distributions.


Thanks!
Adhemar


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] known name outputs shown in /database/files but not in galaxy windows

[Jennifer Jackson]

Hi Angelica,

It appears that you are attempting to directly name the output files. 
Instead, use a variable naming method that permits Galaxy to actually 
name the files accessed by the database, using  with  tags 
to link any working files (with "from_work_dir") and attach attributes 
(including metadata such as "format").


This section and the next is where in the Tool Config wiki you'll most 
likely want to start a review:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set

If you need a new datatype, this is the wiki that explains how to define 
one:

https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes

Hopefully this helps,

Jen
Galaxy team

On 4/3/14 5:13 AM, ANGELICA GOMEZ ROIG wrote:


I have made a wrapper that has a tool that giving it an input file, 
gives you two output files with known extension: .gem and .log
I call the tool with a python file, and I pass it the input file and 
the two output file names for galaxy to show them, but when I look 
into de database/files/000/ i get four files:

dataset_54.dat   (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
So,what I'm getting in the galaxy interface is  _54.dat and _55.dat, 
both empty, instead of _54.dat.gem and _54.dat.log that are the good 
ones.  How can I fix these?

Thanks



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Output file to history

[Jennifer Jackson]

Hi Sebastian,

I'm going to move this over to the galaxy-...@bx.psu.edu mailing list so 
that it reaches the development community effectively. I personally do 
not know the answer, but I am sure we can get you some help.


Best,

Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists

On 3/21/14 9:28 AM, Sebastian Luna Valero wrote:


Dear All,

I am trying to add a new tool in Galaxy and I have the following problem.

Let me explain a simplified example. Let's imagine that my script 
works from CLI as follows:


python script.py --input "input-file" --pattern "output-pattern"

After processing "input-file", the script writes several output files 
and their name is given according to "output-pattern".


The number of output files depends on the content of "input-file". The 
output files are written to the current working directory where 
script.py is located.


In the simplest scenario, I get only one output file in the working 
directory.


My problem is that I would like to see the output files in Galaxy's 
history without modifying the CLI interface.


To solve this problem, I have looked at the wiki page:

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run

and the email here:

http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-history-td4660470.html

However, I think that mine is a different scenario. I do not want to 
add new output parameters in the CLI. I would like Galaxy to bring 
these output files to my history without modifying the CLI options, is 
that possible?


Many thanks in advance for your help!

Best regards,
Sebastian.



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] How to install bowtie2 tool in galaxy

[Jennifer Jackson]

Hi Ravi,

The directory structure for the installation of ToolShed tools changed, 
which is why you have three directories. You perhaps had bowtie2 
installed once before, then reinstalled (without completely removing the 
older version and associated data)? Or updated without resetting the 
metadata? In either case, the ../shed_tools directory is the new one. 
Having this as the path in your .xml configuration files (as Bjoern 
suggested earlier) and moving all contents & data to be under the same 
location will be the simplest global solution ongoing. Links near the 
end of my reply can help explain how-to.


For the specific reason why bowtie2 indices are not working: I noticed 
that the reference genome ".fa" file is not linked from the directory 
containing the indexes. This is required. Adding it in, the same way 
that you did for the bowtie2 indexes, into this dir: 
"/global/referenceData/databases/bowtie2/hg19" will probably solve that 
part of the problem. I didn't see this posted - but I apologize if I am 
duplicating advice already given.


I also tend to advise keeping all data under the same master "data" 
directory - all indexes and sequence data - as symbolic links to 
additional file system paths that are unknown to the 'galaxy user' cause 
a different set of problems. However, that said, this doesn't seem to be 
an issue in your specific case: if the bowtie2 indexes are functioning 
correctly - then environment is set up so that the other dir hierarchy 
where the .fa files are kept must included in the 'galaxy' user's ENV. 
Symbolic links that go outside of the local dir structure are known to 
cause problems unless the ENV config is carefully set up, and to my 
knowledge are best avoided entirely for certain uses such as "upload by 
file path" into libraries.


For reference:

NGS data set-up is described in this wiki - including expected content 
for each type of index:

https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

For examples, you can rsync a genome or two and examine the contents. 
Or, our /location dir and have a look at the .loc files.

https://wiki.galaxyproject.org/Admin/DataIntegration

Tool Shed help (very detailed):
https://wiki.galaxyproject.org/Tool%20Shed
In particular, if you had previously installed repositories (this is not 
clear, just suspected from the duplications), updating the Metadata with 
certain distribution updates can be very important. This has been 
necessary for the last few releases to update to changes. The News Brief 
noted this, and included a link to this wiki page. Also see the "Related 
Pages" lower down on the wiki.

https://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories
This may also be useful:
https://wiki.galaxyproject.org/RepairingInstalledRepositories

Hopefully you have sorted most of this out by now, or this helps!

Jen
Galaxy team


On 3/4/14 12:21 PM, Ravi Alla wrote:

Bjoern,
This is getting frustrating.
There are three places bowtie2_indices.loc file is expected. I really 
don't know which one is the one I should modify.


galaxy-dist/tool-data/bowtie2_indices.loc
galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/96d2e31a3938/bowtie2_indices.loc 

../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/96d2e31a3938/bowtie2/tool-data/bowtie2_indices.loc 



What is the difference between these 3 files?

I changed the 2nd file to include the path to the indices and this 
shows up as a valid preloaded index for tophat2 but does not for 
bowtie2. I also changed the normal bowtie_indices.loc file at the 
second location and this works and I can see the bowtie1 indices for 
that bowtie tool. Currently only the bowtie2 indices are acting up.


I wish this was easier.
Thanks
Ravi.
On Mar 4, 2014, at 11:28 AM, Björn Grüning > wrote:



Hi,

can you check if the file tool_data_table_conf.xml contains an entry 
about bowtie2_indexes ...  or the table shed_data_table_conf.xml ... 
in one of them should be one entry with bowtie2_indexes.


That warning should not be there I think:

> galaxy.tools.parameters.dynamic_options WARNING 2014-03-04 
10:14:33,335 Data table named 'bowtie2_indexes' is required by tool 
but not configured


Hope you can figure it out,
Bjoern

Am 04.03.2014 19:19, schrieb Ravi Alla:

Hi Bjoern,
Please find the bowtie2 and bowtie .loc files. In the paster.log 
file I see these entries for bowtie


galaxy.tools.data DEBUG 2014-03-04 10:14:11,048 Loaded tool data 
table 'bowtie_indexes'
galaxy.tools.data DEBUG 2014-03-04 10:14:11,051 Loading another 
instance of data table 'bowtie_indexes', attempting to merge content.
galaxy.tools.parameters.dynamic_options WARNING 2014-03-04 
10:14:33,335 Data table named 'bowtie2_indexes' is required by tool 
but not configured


And ls -l /global/

Re: [galaxy-dev] Unicode error manipulation of fastq

[Jennifer Jackson]

Hello Brani,

I don't know if you have tried to run other tools on your file, or if 
you have tried this same operation on the public Main instance at 
http://usegalaxy.org, but my guess is that you will run into the same issue.


One path is to convert the UNICODE characters to ASCII. This prior Q&A 
covers the details. The included link to the Trello card is still active 
and can be followed & up-voted:

http://dev.list.galaxyproject.org/Tool-Error-Failure-Preparing-Job-td4660512.html

There is a longer work-around included in this more recent thread (near 
the end, the dist John is talking about went out Feb 10th). I wouldn't 
be able to help with the details of implementation if you run into 
problems, but John possibly could, if this is something you want to try.

http://dev.list.galaxyproject.org/error-with-unicode-output-td4662783.html

Hopefully one of these works out for you,

Jen
Galaxy team

On 2/21/14 8:04 AM, Cantarel, Brandi L. wrote:

Hi,
I am testing my newly installed galaxy instance.  When I try to use a 
simple tool like fastq_to_fasta, I get the following error:

UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in 
position 693: ordinal not in range(256)
Anyone know how I can fix this?

Thanks!
Brandi


~~~
Brandi Cantarel, PhD
Bioinformatics Research Scientist
Baylor Institute for Immunology Research
Baylor Health Care System
214-820-9064 (office)

This e-mail may contain confidential and/or privileged information. 
This information is intended only for the use of the individual(s) and 
entity(ies) to whom it is addressed. If you are the intended 
recipient, further disclosures are prohibited without proper 
authorization. If you are not the intended recipient (or have received 
this e-mail in error) please notify the sender immediately and destroy 
this e-mail. Any unauthorized copying, disclosure or distribution of 
the material in this e-mail is strictly forbidden and possibly a 
violation of federal or state law and regulations. Baylor Health Care 
System, its subsidiaries, and affiliates hereby claim all applicable 
privileges related to this information.



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Unexpected behaviour when downloading HTML files

[Jennifer Jackson]

Hi Shian,

I can reproduce the behavior on the public Main server (usegalaxy.org) 
as well. It is unintentional to my knowledge. I have opened a bug ticket 
to track the issue, and you can also follow it here: 
https://trello.com/c/Y0K7C7ay


Thanks for reporting the problem! If there is more to share, our 
development team will add more to this thread, and/or to the ticket.


Take care,

Jen
Galaxy team

On 2/22/14 3:20 PM, Shian Su wrote:

Hello,

After updating my local Galaxy instance to the latest stable release, 
I've noticed that clicking the floppy-disk download icon on a history 
item of html type no longer downloads all the files in the relevant 
directory. Instead it opens up the html page with broken links. 
However upon going back into the Galaxy page and clicking download for 
the second time it reverts back to the old behaviour of downloading 
the html directory in a zip file, from the second time onwards it 
maintains this behaviour. Is this how it's intended to work? If so 
then is there intention to remove the ability to download the html 
directory?


Regards,
Shian Su
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Reference Genome in snpEff Tool

[Jennifer Jackson]

Hi Xiaofei,

It is best to keep replied on the mailing list.

First, confirm that you are running the most current version of the 
Galaxy distribution. This should be true by default if the installation 
was just performed.

https://wiki.galaxyproject.org/DevNewsBriefs
https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10

Since you ran into this issue the first time the server was brought up 
(or this appears to be the case), you may have run into a characterized 
issue. On the http://getgalaxy.org page, are two work-arounds for 
installing eggs in under specific usage circumstances. One is for when 
running without internet access (probably not the issue). The other is 
for when using Python 2.7 (my best guess as the problem). Both are 
included about half-way down the wiki page, toward the end of the 'Start 
it up' section:

https://wiki.galaxyproject.org/Admin/GetGalaxy

Please review and see if either if these apply, in particular if the 
second command ("sh run.sh --reload") solves the issue.


Again, please keep feedback on the list, so that the developers can 
assist us going forward as needed,


Jen
Galaxy team

On 2/24/14 9:51 AM, Wang, Xiaofei wrote:

Dear Jen,

I really appreciate for your reply!

We decided to install the local Galaxy for this project. But, when I installed 
it (I followed the instruction on these 2 links, 
http://gmod.org/wiki/Galaxy_Tutorial_2013 and 
https://wiki.galaxyproject.org/Admin/GetGalaxy), I got a problem like this:

$ sh run.sh
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Traceback (most recent call last):
   File "./scripts/fetch_eggs.py", line 37, in 
 c.resolve() # Only fetch eggs required by the config
   File 
"/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", 
line 345, in resolve
 egg.resolve()
   File 
"/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", 
line 195, in resolve
 return self.version_conflict( e.args[0], e.args[1] )
   File 
"/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", 
line 226, in version_conflict
 r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )
   File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py",
 line 576, in resolve
 raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a
Fetch failed.

It seems a problem with the Python '"eggs". But, when I checked the version of 
Python, it is:
$ python --version
Python 2.7.6

Could you help me about what is the problem with the installation?

Thank you so much!

Best,

Xiaofei


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error in SICER tool

[Jennifer Jackson]

Hello Nikos,

This is a known issue after the recent tool migrations. The ticket is 
here: https://trello.com/c/h9LSdfdS


The root cause of the error is a missing fortran library. If you click 
on the "eye" for the associated log dataset, and scroll down through the 
full report down to the "Warnings" section: the details are at the 
start, before any other warning are reported. The "missing file" errors 
are all secondary issues related to the missing library.


Our team is actively working on a solution. Not just for the public Main 
Galaxy instance, but for the Tool Shed repository installed dependencies 
(to my knowledge). Follow the ticket and the tool shed repository for 
updates.


This is important correction, but "up-votes" from our community also are 
considered when setting priorities.

https://wiki.galaxyproject.org/Issues

Hopefully this helps to explain the issue,

Jen
Galaxy team

On 2/13/14 4:20 AM, Nikos Sidiropoulos wrote:

Hi all,

I'm getting the following error whenever I'm trying to run SICER

Traceback (most recent call last):
   File 
"/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py
  
", 
line 158, in 
 if __name__=="__main__": __main__()
   File 
"/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py
  
",
 line 154, in __main__
 raise e
IOError: [Errno 2] No such file or directory: 
'/NextGenSeqData/galaxy-data/database/tmp/tmpHPGhcN/input_bed_file-W200-G600-E0.01.scoreisland'

Do you know if there's a workaround for this error?

I have installed SICER from the toolshed (devteam)

Bests,
Nikos


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)

[Jennifer Jackson]

Hi Xiaofei,

I just replied to the other thread about this same question, and left 
you on the cc. Please check out the cloud option - this is intended to 
be useful for those that do not want to invest in a local server or 
manage the associated administrative tasks. If you are working in on a 
project related to academic research, be aware the Amazon has a grant 
program that can help with the costs there (Galaxy is free of course!). 
More details about this are on their web site.

http://usegalaxy.org/cloud
http://aws.amazon.com/grants/

Good luck with your project!

Jen
Galaxy team

On 2/14/14 9:39 AM, Wang, Xiaofei wrote:

Dear,

Is it possible to use SnpEff with genomes of other species (e.g. 
Drosophila) other than C.elegan on galaxy website (not local)? It 
seems the only option for the genome menu (Caenorhabditis elegants : 
WS220.64).


In fact, I am trying to use CloudMap (the EMS Variant Density Mapping 
workflow) to analyze data for Drosophila. So, I have to edit the 
workflow based on my own data. For SnpEff on the workflow, I tried to 
change "Genome" to other species from Caenorhabditis elegants : WS. 
But, there is no other options. Then, I changed it "to be set at 
runtime". When I run the workflow, I still can not change it to other 
species. Then, I went to see the SnpEff tool on galaxy website and 
found that there is no other options for "Genome" option.


So, could you help me about this? Could I use SnpEff and CloudMap (the 
EMS Variant Density Mapping workflow) other than worm? Or, I have to 
install galaxy locally for this objective?


Thank you so much!

Have a nice day!


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Reference Genome in snpEff Tool

[Jennifer Jackson]

Hi Clint, Xiaofei,

There are no current plans to include additional genomes to the SnpEff 
tool on the public Main Galaxy instance at http://usegalaxy.org.


The best solution is to either run a local Galaxy (with sufficient 
resources) or what is probably easier and more practical for many 
scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. 
The tool wrapper is in the Tool Shed, so it can be installed and used 
within your Galaxy, where you can add in any genome that you want that 
has the appropriate reference data available.


Help to get started is in these links:
https://wiki.galaxyproject.org/BigPicture/Choices
https://wiki.galaxyproject.org/Tool%20Shed

Hopefully one of these solutions will work out for both of you!

Jen
Galaxy team

On 2/17/14 8:20 AM, Wang, Xiaofei wrote:

I have the same question. But, I want to use it on Drosophila and use SnpEff 
for CloudMap pipeline.

From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Clint Christensen [cli...@txbiomedgenetics.org]
Sent: Monday, February 17, 2014 10:01 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Reference Genome in snpEff Tool

Howdy!

I only see the "Caenorhabditis elegans: WS220.64" reference genome listed in the 
"Genome" drop down menu in the snpEff tool.  If possible, I would like to use the latest 
human genome hg19.  Can it be added as an option?  Thanks in advance.

Not: I did follow the link to the developer's site, but would prefer to use the 
tool from within Galaxy.

Clint Christensen
Research Assistant, Department of Genetics
Texas Biomedical Research Institute
7620 NW Loop 410
San Antonio, TX  78245
210-258-9779
cli...@txbiomedgenetics.org



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Feb 10, 2014 Galaxy Distribution & News Brief

[Jennifer Jackson]

Feb 10, 2014 Galaxy Distribution & News Brief


//
*CompleteNews Brief 
*


*Highlights:*

 * Visualization upgrades, including Trackster CSS styling
 * Multiple Tools migrated to the Tool Shed for a leaner distribution
 * Redesign of UI rendering: new icons, new font, history pane updates
 * API functionality upgrades featuring a new master admin API key and
 * Tool Shed updates a focus on repository metadata, displays,
   installs, and tests
 * Over 35 new community contributions added

http://getgalaxy.org 

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org 

new:   $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade:   $ hg pull
   $ hg update release_2014.02.10

/Thanks for using Galaxy!/

The Galaxy Team 

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Install tools from Toolshed

[Jennifer Jackson]

Hello Shivani,

The problem is either related to 3rd party cookies being enabled or a 
missing configuration in the universe.wsgi.ini file. This thread, in the 
second part, provides the full solution:


http://dev.list.galaxyproject.org/Invalid-Galaxy-URL-None-Installing-Tools-Shed-td4659659.html

Also, make sure you are running the latest version of Galaxy and 
followed the required upgrade procedures before trying.

https://wiki.galaxyproject.org/DevNewsBriefs/

I am moving this over to the galaxy-...@bx.psu.edu mailing list, in case 
more follow-up is needed. That is the best list to use for 
troubleshooting local install / tool shed questions.


Take care,

Jen
Galaxy team

On 1/25/14 12:36 PM, Malik, Shivani wrote:

HI,
I am trying to install Deseq from the toolshed. I get the 
message:Repository installation is not possible due to an invalid 
Galaxy URL: *None*. You may need to enable cookies in your browser.
I have enabled the cookies and tried both on Firefox and Chrome but 
could not get it to work. Can you help me on this?

Thanks
Shivani


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] wigToBigwig error

[Jennifer Jackson]

Hi Rui,

This error probably means that the binaries from UCSC are not installed 
or the path to the tools is incorrect. "ucsc_tools" is a package 
requirement for the tools that use these binaries in the .xml portion of 
the wrapper (for those in the dist/devteam).


If you are running your own instance, without any dependencies on other 
institutional resources or repositories, then any binaries needed should 
in most cases come from UCSC in the Downloads area under source and be 
installed. Some wrappers are in the distribution (such as wigToBigWig in 
galaxy-dist / tools / filters ), but there are others are in the tool shed.

http://hgdownload.cse.ucsc.edu/admin/exe
http://usegalaxy.org/toolshed

Where the other repo comes in, I am not sure. Maybe from a wrapper 
installed from the Tool Shed (or another source) that needs a UCSC 
binary. If it is dependent on a particular version, that could be a 
reason for a distinct repo. Contacting the wrapper author may help to 
clarify. Tools in the distribution and from "devteam" in the Tool Shed 
all use the standard UCSC source to my knowledge.


Maybe others will add in comments to this thread, if they recognize 
this. Or, your sysadmin can help if you contact them, if there shared 
resources to make use of.


On 1/15/14 10:30 AM, ruiwang.sz wrote:

Hi Jennifer,

Thanks for the note.

A related question, do we have a 'ucsc_tool'? I sometimes saw the 
warning of failed dependency on ucsc_tool, but I'm not sure what it 
is. I found that there are many binary/script utilities:


https://github.com/adamlabadorf/ucsc_tools

should I install all these by running

python setup.py install

or I could just copy all those executables to my own utility dir?

Thanks,
Rui


On Wed, Jan 15, 2014 at 7:51 AM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote:


Hello Rui,

The problems you are describing have to do with the format of the
input wig dataset.

It looks as if you have corrected the chromosome names to be
identical to the reference genome build used (required). There are
options to overcome the other issues:

1. verify that your data has no browser lines, and has track and
definition lines in the correct format. UCSC is the definitive
source for this info, as both the underlying tool and this format
were developed by them. Links to their information and the general
format rules in Galaxy can be found here
https://wiki.galaxyproject.org/Learn/Datatypes#Wig_and_bigWig

2. send only a single wig file to the tool at a time, when using
the Galaxy wrapper.

3. use the 'full parameter' option 'Clip chromosome positions:' to
removing overhanging coordinates (known to be produced by several
common tools). This is after confirming that the build is correct
- overhanging coordinates can be a clue that there is a genome
mismatch problem.
https://wiki.galaxyproject.org/Support#Reference_genomes

4. note that variable step data comes in two formats fixed and
variable - and that variable has two format versions, those with a
a span definition and those without (see examples in wig examples
in #1). I have only seen this tool run successfully, in Galaxy, on
the type without "span" included. If you find that the span
variable is problematic after correcting any other format issue
issues, switch to the format without span.

Good luck,

Jen
Galaxy team


On 1/14/14 9:52 PM, ruiwang.sz <http://ruiwang.sz> wrote:

Hi All,

I'm having an error at this:

*Dataset 18: Wig/BedGraph-to-bigWig on data 12*

Tool execution generated the following error message:

grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe

..
put: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe

..

grep: writing output: Broken pipe

grep: write error

Error running wigToBigWig.

The tool produced the following additional output:

hashMustFindVal: '1' not found


I searched and found this link:



http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767


which says that there is a naming convention difference.


I followed what he did and replaced chrom=1 to chrom=chr1 etc,
now it goes further, but

still dies with error:


line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276760

line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276770

line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276780

line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases,
but item ends at 195276790

line 18020172 of /tm

Re: [galaxy-dev] wigToBigwig error

[Jennifer Jackson]

Hello Rui,

The problems you are describing have to do with the format of the input 
wig dataset.


It looks as if you have corrected the chromosome names to be identical 
to the reference genome build used (required). There are options to 
overcome the other issues:


1. verify that your data has no browser lines, and has track and 
definition lines in the correct format. UCSC is the definitive source 
for this info, as both the underlying tool and this format were 
developed by them. Links to their information and the general format 
rules in Galaxy can be found here

https://wiki.galaxyproject.org/Learn/Datatypes#Wig_and_bigWig

2. send only a single wig file to the tool at a time, when using the 
Galaxy wrapper.


3. use the 'full parameter' option 'Clip chromosome positions:' to 
removing overhanging coordinates (known to be produced by several common 
tools). This is after confirming that the build is correct - overhanging 
coordinates can be a clue that there is a genome mismatch problem.

https://wiki.galaxyproject.org/Support#Reference_genomes

4. note that variable step data comes in two formats fixed and variable 
- and that variable has two format versions, those with a a span 
definition and those without (see examples in wig examples in #1). I 
have only seen this tool run successfully, in Galaxy, on the type 
without "span" included. If you find that the span variable is 
problematic after correcting any other format issue issues, switch to 
the format without span.


Good luck,

Jen
Galaxy team

On 1/14/14 9:52 PM, ruiwang.sz wrote:

Hi All,

I'm having an error at this:

*Dataset 18: Wig/BedGraph-to-bigWig on data 12*

Tool execution generated the following error message:

grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe

..
put: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe

..

grep: writing output: Broken pipe

grep: write error

Error running wigToBigWig.

The tool produced the following additional output:

hashMustFindVal: '1' not found


I searched and found this link:


http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767


which says that there is a naming convention difference.


I followed what he did and replaced chrom=1 to chrom=chr1 etc, now it 
goes further, but


still dies with error:


line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276760


line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276770


line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276780


line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276790


line 18020172 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276800


line 18020173 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276810


line 18020174 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276820


line 18020175 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276830


line 18020176 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276840


line 18020177 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276850


line 18020178 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276860


line 18020179 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276870


line 18020180 of /tmp/t3: chromosome chr1 has 195276750 bases, but 
item ends at 195276880


Unrecognized line 18020181 of /tmp/t3:

variableStep chr10 span=10


Error running wigToBigWig.


The command line is: wigToBigWig  /tmp/t3 
/home/bioinfoadmin/app/galaxy-dist/tool-data/shared/ucsc/chrom/ucsc_gg4.len 
/home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_769.dat 
-clip 2>&1 || echo "Error running wigToBigWig." >&2



Quite puzzled...wondering if anyone has seen it before and could give 
me a hand. :-) I'll really appreciate!



Thanks,

Rui




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] password problem

[Jennifer Jackson]

Hello Andrea,

Are you still having login issues?

The first thing to double check is that you confirmed your registration. 
Did you get an email with a link? I am wondering because the address you 
have below differs in capitalization from the address you are sending 
from, and your Galaxy account has the capitalized version. This would 
most likely cause emails to fail delivery, and therefore the account 
would not be confirmed (and able to execute jobs).


Still, you should be able to log in. Again, make sure that the proper 
case is used when loggin in - the same as for original registration = 
capitolized. Once logged in, you can update the email to be all lower 
case. This will ensure that you get emails from our team: registration 
confirmation to start with, but later on if our administrator needs to 
reach you (and this is infrequent), those are emails that you definitely 
want to get.


We are checking our records here, but I wanted to make contact as well, 
since it is not clear how far you got in the process, and the case issue 
with the email needs to be addressed anyway (and is good advice for 
others to know about).


You can email back direct if you want as we work through this,

Best,

Jen
Galaxy team



On 1/9/14 4:06 AM, Szendroi Andrea (KING'S COLLEGE HOSPITAL NHS 
FOUNDATION TRUST) wrote:


To Whom It May Concern:

Yesterday, I successfully registered to the Galaxy from my home 
computer using my: andrea.szend...@nhs.net 
 email.


Today, I tried to logon again from my work computer and it did not 
recognize my password so I tried to reset it and to send my new 
password to the same email but no email came (I have even checked my 
junk box). I have tried to reset it several times without any success.


Could you please help me?

Many thanks,

Andrea




This message may contain confidential information. If you are not the 
intended recipient please inform the

sender that you have received the message in error before deleting it.
Please do not disclose, copy or distribute information in this e-mail 
or take any action in reliance on its contents:

to do so is strictly prohibited and may be unlawful.

Thank you for your co-operation.

NHSmail is the secure email and directory service available for all 
NHS staff in England and Scotland
NHSmail is approved for exchanging patient data and other sensitive 
information with NHSmail and GSi recipients
NHSmail provides an email address for your career in the NHS and can 
be accessed anywhere





___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Help Needed

[Jennifer Jackson]

Hello Elsayed,

Your protocol below seems to be a mix of a variant detection and an 
RNA-seq workflow. To build a workflow for RNA-seq, you will want to 
compare your steps with the protocols in the link that I sent you.


If you want more examples, many more can be found here (for both RNA-seq 
and variant analysis, these are distinct analysis). Some have workflows 
that you can import and use directly or modify.


   https://wiki.galaxyproject.org/Learn#Other_Tutorials

   Shared Data -> Published Pages

In particular, there is a sample workflow in this tutorial that will 
help you to understand what the different steps are for and what order 
they go in.

https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Best,

Jen
Galaxy team



On 1/3/14 10:57 AM, Elsayed Hejazy wrote:

*Dear Dr. Jennifer,*
A lot of thanks for your reply its really mean alot for me.
i am still NGS junior i trying to do the following steps kindly give 
me the right order for these procedures
Data Description: i have to samples each sample consists of 14 FASTQ 
file (7 forward and 7 reverse ) i think this mean its paired end from 
Illumina then i will try the following workflow to got best results
1- Drag tow input dataset into workflow one for forward sequences file 
and one for reverse to use paired end option in TOPHAT tool later and 
when i run this workflow i will select multiple selection for the 7 
forward files to analyse all of them at the same time
2- Drag FASTQC and link with last step for each to got if these file 
may be illmina 1.8 version or older.
3- Drag FASTQ Groomer and link with last step if files older than 1.8 
version to prepare as .FASTQSANGER format.
4- Drag Filter FASTQ and link with last step to remove redundancy of 
sequences.

5- Drag FASTQ trimmer to remove unwanted ends of sequenced may occur
6- Drag Manipulate FASTQ and link with last step (i dont know why).
the above six steps done twice to generate to files as output to make 
as input for the following steps.
7- Drag TOPHAT for illumina and make it accept paired end files and 
link each file generated from QC to TOPHAT this step used to align and 
map with reference genome.
8- Drag Cufflinks and link with aligned BAM file generated from TOPHAT 
to create an assembly
9- Drag Cuffmerge and link with GTF file from Cufflinks this step to 
merge all assemblies generated in Cufflinks
10- Drag Cuffcompare and link with last step to got detailed reports 
for accuracy of all generated assemblies.
11- Drag MPileup and link with TOPHAT BAM file to generate file 
containing SNPs sites.
12- Drag Pileup-to-Interval and link with MPileup step to filter the 
number of output SNPs to successive one or the most accurate. (i dont 
know what is the difference between this tool and Filter Pileup).
- i dont know what is the tools used to know the copy number variation 
CNV
i need to know how to separate human sequences from sample may 
infected with any other sequences (is this at alignment stage)
i need to know the perfect order of steps if this order is not 
completely right.


Is this what i should do to make a good NGS workflow got all possible 
information form dataset


Really i am so so so sorry for disturbance - waiting your reply
Best Regards,
elsayed



On Thu, Jan 2, 2014 at 6:05 PM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote:


Hello Elsayed,

Protocol help for RNA-seq analysis can be found here:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

The QA/QC steps should be done before mapping, on individual
datasets (such as replicates) or on partial or merged datasets as
needed (if that is how the data was sequenced, just be
consistent). Only keep in mind that the larger the dataset, the
more compute some of these steps can require.

Hopefully this helps,

Jen
Galaxy team


On 1/1/14 1:32 AM, Elsayed Hejazy wrote:

i need to know more about the order of steps for RNA Seq data
analysis
Is alignment and assembly should done first to combine all FASTQ
reads into one file and start analysis or i should do Quality
Control ,filtering  , trimming and manipulation first and do
alignment and assembly at the end of analysis to use tophat for
example or any other analysis tools in Galaxy

Thank you
elsayed


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


-- 
Jennifer Hillman-Jackson

http://galaxyproject.org




--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by usi

Re: [galaxy-dev] ODoSE - error when using exclusively 'external' genomes

[Jennifer Jackson]

Hello Jen,

For this problem, you will need to reach the support or administrators 
for this public server.

https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE

The authors of the primary publication are probably the best contacts (I 
couldn't locate any others). You can find these linked from the paper, 
which is open source, but I will also send them to you direct (to avoid 
posting to a public list without permission first).


Best,

Jen
Galaxy team

On 12/31/13 9:18 AM, Jen wrote:

hello,

I've run across a possible bug in ODoSE that is preventing me from analyzing my 
data.  I've scoured the various help documentation without luck, so I'm writing 
you.

I'm using the program via this site:
http://www.odose.nl/

The history showing the steps below is here:

http://www.odose.nl/u/publ/h/unnamed-history

The problem is this: I'm unable to work with a set of genomes that is exclusively 
"user-generated" (i.e., external, and uploaded from my local drive).

To illustrate this problem with an example, I downloaded the .ffn files for 
four published genomes NCBI's ftp site.  (This way, I'm sure my 'external' 
files are formatted correctly.)

I've tried to follow these instructions from http://www.odose.nl/ (Analyze Data 
tab) -


"User-generated whole-genome data not yet archived in GenBank can be uploaded to be 
analysed separately or in conjunction with published genomes. To do this, first create a new 
history: in the right ‘History’ pane go to Options > Create New. In the left ‘Tools’ pane go 
to Get Data > Upload File and select one or multiple .ffn files from your computer and click 
‘Execute’..."

This worked fine.


"Go to Divergence > Upload genomes in the ‘Tools’ pane, press the ‘Add new genome’ 
button, specify a genome label and press ‘Execute’ for each genome to be included…"

I was unable to find a "Divergence" option in the Tools pane.  So, I assumed this should be 
O'DoSE > Upload Genomes, in the Tools Pane.  Using this function, I uploaded each genome and 
selected "Execute."


"Proceed to the Workflow menu to add listed genomes and/or to specify input 
settings…"

Perhaps this is my downfall, but I was unable to see how to add genomes in the 
Workflow menu.

At this point, I had uploaded four genomes, and attempted to select the first option in the analysis: 
"Extract & Translate Genes."  I chose the option of selecting my external genomes, but the analysis 
failed, giving the error "History does not include a dataset of the required format/build" error.  This 
error appears within the "Genbank Project ID's" box.  In this case, I have no Genbank Project ID's, 
because all data are external genomes.

Interestingly:

The problem is solved by selecting at least one genome from the Complete Microbial Genomes 
table.  Selecting one genome generates a Project ID list.  I am then able to perform 
"Extract & Translate Genes" and all further functions, acting on the set of 
external genomes and the one selected (internal) genome.   I've tried this several times, 
with different external genome files.  I can successfully analyze dozens of external genomes, 
but _only if_ at least one 'internal' genome is selected as well.


I need to run an analysis on a set of genomes that is exclusively unpublished, so the 
data will be entirely "external" genomes. Including a published genome will 
throw off the comparisons we need to make.

Based on the ODoSE instructions above (that user-generated whole-genome 
data...can be uploaded to be analysed separately or in conjunction with 
published genomes), I sense I should be able to use exclusively 'external' 
genomes in an analysis.  Do you have any suggestions on how I can do this?   
Any advice would be much appreciated.

thank you,
Jen

(Apologies to the moderator for the earlier version of this message that was 
too large.  Above, I've removed the attachments showing screen shots.  I hope 
the problem is clear from the History link above.)


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Can REMOTE_USER be changed to another header variable?

[Jennifer Jackson]

Hi Prakash,

You are on the thread so you should get direct replies. And you can 
review any of our mailing list postings by following the links here 
under "Archives":

https://wiki.galaxyproject.org/MailingLists#The_lists

Subscribing is optional, for posting or viewing.

Thanks!

Jen
Galaxy team

On 1/2/14 8:12 AM, Velayutham, Prakash (Prakash) wrote:

Hi,

I guess I would have to subscribe to that list to get status updates?

Thanks,
Prakash

On Jan 2, 2014, at 11:09 AM, Jennifer Jackson <mailto:j...@bx.psu.edu>>

 wrote:


Hello Prakash,
I am going to move this over to the galaxy-...@bx.psu.edu mailing 
list where it will have greater visibility within our development 
community.

Best,
Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists#The_lists

On 1/2/14 7:27 AM, Velayutham, Prakash (Prakash) wrote:

Hi,

We have a SSO environment provided by Oracle Fusion products and for 
some reason, they don't like to send over HTTP_REMOTE_USER as a 
header variable to downstream servers. I have seen it before with 
other web sites I have integrated with Oracle Access Manager. Is 
there a way Galaxy can accept another HEADER variable than 
REMOTE_USER for its external authentication?


As an extension:

  * With just enabling HTTP_REMOTE_USER as a header variable from an
external authenticator, Galaxy works without any issues. I tried
this with a default Apache/mod_ldap/mod_authnz_ldap setup.
  * However, when I mix the Oracle gateways into the mix, things
break down.
  o I made OAM send HTTP_AUTH_USER over to Galaxy.
  o I changed all instances of REMOTE_USER to AUTH_USER in the
installed location of Galaxy in my server.
  o Authentication works fine, but I get issues with HISTORY
part of Galaxy (below), when I access a workflow or
basically any part of Galaxy that depends on HISTORY


  Error Traceback:

View as: Interactive 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>  | 
Text 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>  | 
XML 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
(full) 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>

⇝ |AttributeError: 'NoneType' object has no attribute 'user'|
URL: 
http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False
Module weberror.evalexception.middleware:*364* in |respond| Attachment.jpeg> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
view 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>
|>> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>app_iter 
*=* self*.*application*(*environ*,* detect_start_response*)*|
Module paste.recursive:*84* in |__call__|  
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
view 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>
|>> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>*return* 
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.middleware.remoteuser:*91* in |__call__| 
 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
view 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>
|>> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>*return* 
self*.*app*(* environ*,* start_response *)*|
Module paste.httpexceptions:*633* in |__call__| Attachment.jpeg> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
view 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>
|>> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#>*return* 
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*132* in |__call__| Attachment.jpeg> 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False#> 
view 
<https://galaxy.research.cchmc.org/dataset/list?sort=-update_tim

[galaxy-dev] Can REMOTE_USER be changed to another header variable?

[Jennifer Jackson]

  
  
Hello Prakash,
I am going to move this over to the galaxy-...@bx.psu.edu mailing
list where it will have greater visibility within our development
community.
Best, 
Jen
Galaxy team
https://wiki.galaxyproject.org/MailingLists#The_lists

On 1/2/14 7:27 AM, Velayutham, Prakash
  (Prakash) wrote:


  
  Hi,
  
  
  We have a SSO environment provided by Oracle Fusion products
and for some reason, they don't like to send over
HTTP_REMOTE_USER as a header variable to downstream servers. I
have seen it before with other web sites I have integrated with
Oracle Access Manager. Is there a way Galaxy can accept another
HEADER variable than REMOTE_USER for its external
authentication?
  
  
  As an extension:
  
  
  

  With just enabling HTTP_REMOTE_USER as a header variable
from an external authenticator, Galaxy works without any
issues. I tried this with a default
Apache/mod_ldap/mod_authnz_ldap setup.
  However, when I mix the Oracle gateways into the mix,
things break down.

  I made OAM send HTTP_AUTH_USER over to Galaxy.
  I changed all instances of REMOTE_USER to AUTH_USER in
the installed location of Galaxy in my server.
  Authentication works fine, but I get issues with
HISTORY part of Galaxy (below), when I access a workflow
or basically any part of Galaxy that depends on HISTORY

  



  
  

  Error Traceback:

  View as:
  Interactive  |  Text  |  XML (full)

  ⇝ AttributeError:
'NoneType' object has no attribute 'user'

  URL: http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-deleted=False

  Module weberror.evalexception.middleware:364 in respond      view
  >>  app_iter = self.application(environ, detect_start_response)


  Module paste.recursive:84 in __call__      view
  >>  return self.application(environ, start_response)


  Module galaxy.web.framework.middleware.remoteuser:91 in __call__      view
  >>  return self.app( environ, start_response )


  Module paste.httpexceptions:633 in __call__      view
  >>  return self.application(environ, start_response)


  Module galaxy.web.framework.base:132 in __call__      view
  >>  return self.handle_request( environ, start_response )


  Module galaxy.web.framework.base:190 in handle_request      view
  >>  body = method( trans, **kwargs )


  Module galaxy.web.framework:98 in decorator      view
  >>  return func( self, trans, *args, **kwargs )


  Module galaxy.webapps.galaxy.controllers.dataset:555 in list      view
  >>  status, message = self._copy_datasets( trans, hda_ids, target_histories )


  Module galaxy.webapps.galaxy.controllers.dataset:1127 in _copy_datasets      view
  >>  if user != history.user:

AttributeError: 'NoneType' object has no attribute 'user'

  
  
  
  Thanks,
  Prakash
  
  
  
  ___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
  

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Help Needed

[Jennifer Jackson]

Hello Elsayed,

Protocol help for RNA-seq analysis can be found here:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

The QA/QC steps should be done before mapping, on individual datasets 
(such as replicates) or on partial or merged datasets as needed (if that 
is how the data was sequenced, just be consistent). Only keep in mind 
that the larger the dataset, the more compute some of these steps can 
require.


Hopefully this helps,

Jen
Galaxy team

On 1/1/14 1:32 AM, Elsayed Hejazy wrote:

i need to know more about the order of steps for RNA Seq data analysis
Is alignment and assembly should done first to combine all FASTQ reads 
into one file and start analysis or i should do Quality Control 
,filtering  , trimming and manipulation first and do alignment and 
assembly at the end of analysis to use tophat for example or any other 
analysis tools in Galaxy


Thank you
elsayed


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Error running CCAT test

[Jennifer Jackson]

Hi Nicola,

This doesn't appear to be a known functional test failure (if I am 
reading the logs right), but I am also not the best resource to 
troubleshoot this particular type of problem. I am going to move this to 
the dev list for more feedback. If you want to add more details about 
your system (local? tracking galaxy-dist or central?) that might help.


Best,
Jen
Galaxy team

On 12/18/13 2:42 AM, Nicolas Lapalu wrote:

Hi,

I tried to run CCAT functionnal test, but I get an exception (same 
problem via web form)
Data are well associated with the hg18 build, which is available in 
test-data/chrom/hg18.len



Error running CCAT.
Traceback (most recent call last):
  File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 41, 
in 

if __name__ == "__main__": main()
  File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 38, 
in main

return stop_err( tmp_dir, e )
  File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 13, 
in stop_err

raise exception
AssertionError: The required chromosome length file does not exist.

Any Idea ?

Thanks, Nicolas




--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Trinity in local

[Jennifer Jackson]

Hello Jorge,

I just replied to your other question on the galaxy-user list with all 
of the details about configuring tools (wrappers vs binaries).


For this tool, the binary components most likely need to be installed 
and configured.


http://trinityrnaseq.sourceforge.net


Best,

Jen
Galaxy team

On 12/17/13 2:17 AM, Jorge Braun wrote:

hi mates,

I have problems to run trinity in local galaxy, because there is no 
executable script.


any ideas?

thank you very much


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

[Jennifer Jackson]

Javier,

This is part of a tool repository that can be installed into a local, 
cloud, or slipstream Galaxy and used there.


http://getgalaxy.org
http://usegalaxy.org/cloud
https://wiki.galaxyproject.org/BigPicture/Choices
http://usegalaxy.org/toolshed
https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance

I am not sure of the size of your files, but if not too large, these 
tools may work just fine on a local install on a laptop. For anything 
larger, a server would be needed for a local or for the easiest set-up, 
use a cloud. For ongoing work, a slipstream Galaxy can be a great 
solution for labs.


Take care,

Jen
Galaxy team

On 12/16/13 7:30 AM, Javier Simon-Sanchez wrote:


Hi Jennifer,

Intersect_bed is exactly what I need. How can I include this on my 
workflows? (sorry for asking so many things. Im new with galaxy)


*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Monday, December 16, 2013 4:03 PM
*To:* Javier Simon-Sanchez; galaxy-...@bx.psu.edu
*Subject:* Re: [galaxy-dev] Count intervals in one file overlapping 
intervals in another file


Hello Javier,

If you would like to see an enhancement for a tool that is sourced 
from the tool shed, then the repository author is the correct person 
to contact. Go to http://usegalaxy.org/toolshed and log in to see 
contact information. The repo name is "bedtools".


The Tool Shed also has an alternate versions of some BedTools, 
including this one. An alternative has an option to set overlap 
length: " bed_intersect".


Also, there are tools in the group "Operate on Genomic Intervals". I 
don't know the details of your query, but these tools may also be helpful.


Best,

Jen
Galaxy team

On 12/13/13 2:41 AM, Javier Simon-Sanchez wrote:

Hello,

I just noticed that when using the above mentioned option, it is
not possible to set a minimum overlap required. This option can be
run in the command line version of BEDtools and I think is
crucial. Could you please implement it in Galaxy?

Thanks a lot.

-

Javier Simón-Sánchez, PhD

Research Scientist

MRC-Holland

Willem Schoutenstraat 6

1057 DN, Amsterdam

The Netherlands




___

Please keep all replies on the list by using "reply all"

in your mail client.  To manage your subscriptions to this

and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/

  


To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/



--
Jennifer Hillman-Jackson
http://galaxyproject.org


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

[Jennifer Jackson]

Hello Javier,

If you would like to see an enhancement for a tool that is sourced from 
the tool shed, then the repository author is the correct person to 
contact. Go to http://usegalaxy.org/toolshed and log in to see contact 
information. The repo name is "bedtools".


The Tool Shed also has an alternate versions of some BedTools, including 
this one. An alternative has an option to set overlap length: " 
bed_intersect".


Also, there are tools in the group "Operate on Genomic Intervals". I 
don't know the details of your query, but these tools may also be helpful.


Best,

Jen
Galaxy team

On 12/13/13 2:41 AM, Javier Simon-Sanchez wrote:


Hello,

I just noticed that when using the above mentioned option, it is not 
possible to set a minimum overlap required. This option can be run in 
the command line version of BEDtools and I think is crucial. Could you 
please implement it in Galaxy?


Thanks a lot.

-

Javier Simón-Sánchez, PhD

Research Scientist

MRC-Holland

Willem Schoutenstraat 6

1057 DN, Amsterdam

The Netherlands



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] inconsistent BAM-to-SAM behavior

[Jennifer Jackson]

Repost: Mike, please reply to the list threaded question to help us 
track and to permit the entire Galaxy community to learn and contribute 
to Q/A. Thanks!

-

Thanks for the response Jen!

Answers to your questions below.

1. It should be the newest version of Galaxy
2.   We did make production server changes but I'll check the admin
   part again
3. This might be the problem.  I tried to install
   package_samtools_0_1_19 but it failed, then I installed
   package_samtools_0_1_18 which succeeded, and lastly I installed
   bam_to_sam
4. I have not tried the main galaxy instance yet.

I did mean the "same" file. I just turned off autoscaling to simplify 
things.
I'll get back to after: unistalling package_samtools_0_118 and 
bam_to_sam and then just installing bam_to_sam and reviewing the how our 
production server is set up.

Thanks
Mike



On 12/10/13 3:03 PM, Jennifer Jackson wrote:

Hi Mike,

I am moving this over to the galaxy-...@bx.psu.edu mailing list as it 
concerns a local install. This is the best way to make contact with 
others working with the same type of Galaxy.

https://wiki.galaxyproject.org/MailingLists

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
  initial install: http://getgalaxy.org
  next steps are under: https://wiki.galaxyproject.org/Admin
  in particular: 
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer


3 - You installed SAMTools from the Tool Shed? The config is correct? 
And are running the latest version?

https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

4 - When you run the same dataset(s) through on the public Main Galaxy 
instance at http://usegalaxy.org, is it successful or does it fail?


I wasn't sure if you meant that the same file will fail and then pass, 
or if some fail and some pass. If you could clarify that, it would 
help. It could mean the difference between a processing problem 
(pointing to a config or other issue) and a simple memory problem 
(where allocating more could help). Please keep all replies on the 
mailing list with a cc.


Thanks!

Jen
Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:

Hi,

I have run some top hap output through the samtools BAM-to-SAM 
wrapper. It creates the SAM file about 50% of the time. The rest of 
the time it makes an empty file. In this case if I just rerun it 
often works. I was wondering if anyone else has seen this behavior. I 
am using a cloud server and think  I might need to change some 
settings. This causes my workflow to fail for many libraries so I 
also interested in any workarounds anyone has figured out.

Thanks in advance for any help.
Cheers
Mike

--
Jennifer Hillman-Jackson
http://galaxyproject.org


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] inconsistent BAM-to-SAM behavior

[Jennifer Jackson]

Hi Mike,

I am moving this over to the galaxy-...@bx.psu.edu mailing list as it 
concerns a local install. This is the best way to make contact with 
others working with the same type of Galaxy.

https://wiki.galaxyproject.org/MailingLists

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
  https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
  initial install: http://getgalaxy.org
  next steps are under: https://wiki.galaxyproject.org/Admin
  in particular: 
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer


3 - You installed SAMTools from the Tool Shed? The config is correct? 
And are running the latest version?

https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
  https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

4 - When you run the same dataset(s) through on the public Main Galaxy 
instance at http://usegalaxy.org, is it successful or does it fail?


I wasn't sure if you meant that the same file will fail and then pass, 
or if some fail and some pass. If you could clarify that, it would help. 
It could mean the difference between a processing problem (pointing to a 
config or other issue) and a simple memory problem (where allocating 
more could help). Please keep all replies on the mailing list with a cc.


Thanks!

Jen
Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:

Hi,

I have run some top hap output through the samtools BAM-to-SAM 
wrapper. It creates the SAM file about 50% of the time. The rest of 
the time it makes an empty file. In this case if I just rerun it often 
works. I was wondering if anyone else has seen this behavior. I am 
using a cloud server and think  I might need to change some settings. 
This causes my workflow to fail for many libraries so I also 
interested in any workarounds anyone has figured out.

Thanks in advance for any help.
Cheers
Mike


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] ClustalW

[Jennifer Jackson]

Hi Sheri,

To confirm, you are using the public Main Galaxy instance at 
http://usegalaxy.org?


Is the dataset "red" (an error)? If so, would you mind submitting this 
as a bug report?


If not red, the next best option is to share the history. If you could 
generate a link and email that back, would be great (to just me, you 
don't need to share with the list).

http://wiki.galaxyproject.org/Learn/Share

Thanks for reporting the problem,

Jen
Galaxy team

On 12/3/13 3:16 PM, Sheri Zada wrote:

Hi there,

I think there is an error with ClustalW. I uploaded a fasta file 
containing two sequences of the luciferin gene from two different 
organisms. This site: http://www.ch.embnet.org/software/ClustalW.html
works for the same files, but I would like to keep everything on 
galaxy because I want to produce a workflow for a page I am creating 
with a project partner.
The error that comes up is : "clustalw2 not found", and the file is 
empty.

Any help would be much appreciated. Thanks!

Sheri Zada


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error while trying to extract DNA

[Jennifer Jackson]

Hi Alan,

My guess is a format issue with the input. These are usually solved easily.

Is this occurring on the public Main server at usegalaxy.org? If not, 
can you duplicate the problem there?
Please share a link to the history (can send directly to me) with the 
problem if you do this and it is problematic.


The other option is for you to review the input format very carefully 
yourself. Make sure that you are following a very strict BED format with 
this tool. Click on the pencil icon to check the column assignments and 
modify the datatype as needed. The database assignment is also important 
- this is what the tool uses to know the target reference genome, unless 
you are using a custom reference genome (in which case you want this to 
be set to "unspecified"). Custom genomes can have all sorts of issues, 
but in general sticking with strict fasta format is the key to success.


Hopefully one of these will work out!

Jen
Galaxy team

On 11/21/13 7:09 AM, Alan WiIliams wrote:

Hi,
I am new here.  I have a interval file with the columns chr,start,end.
When I run it I get 10 warnings, 1st is: Unable to fetch the sequence
from '172591712' to '3209' for chrom 'chr5'. Skipped 10 invalid lines,
1st is #1, "chr5 172591712 172594921" Which doesn't make sense.  Can
someone help?
Thanks,



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

[Jennifer Jackson]

Hi Karen,

HyPhy is problematic right now. Reports of failing on MAF input are the 
most recent on the public server, but the error you see is not outside 
of the scope of the problem (to my knowledge). This is the open ticket 
with more details:

https://trello.com/c/9TMF2aJl

I do not have an ETA for a correction.

Best!

Jen
Galaxy team

On 11/26/13 9:16 PM, Karen Miga wrote:


Hello - I am running to errors when trying to run Clustalw and HyPhy 
on our cloudman instance.


(1) Clustalw:  The program completes without error and produces an 
empty file and a log file that states "/bin/sh: 1: clustalw2: not found"


Searching around a bit I am not seeing clustalw2 previously installed. 
 I am happy to do it if need be, however, I wanted to check in and see 
if I am overlooking the directory or an easy fix.
If I do need to install clustalw,  I would prefer to use 
clustalw-omega, but was not sure if I needed to script a brand new 
wrapper or if I could use the previous one that came with galaxy image.


(2) HyPhy:  The cloud the link was initially broken.  I changed it to 
the correct path:


sudo ln -sfn /mnt/galaxy/tools/hyphy/default 
/mnt/galaxy/galaxy-app/tool-data/HYPHY


I am using a fasta alignment file of 6 protein sequences (566 AA each) 
as a test case (*also fails with nucleotide alignments).
It runs briefly and then issues an error statement "Single Alignment 
Analyses Segmentation fault (core dumped)".


Thank you in advance,

Karen




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] how to add openstack in biocloudcentral ?

[Jennifer Jackson]

Hello Zeeshan, Let's post this over to the proper list, 
galaxy-...@bx.psu.edu, and see if that helps.
You could also contact Brad, the git repository owner, directly about 
questions that involve biocloud.

Best,
Jen
Galaxy team
http://wiki.galaxyproject.org/MailingLists#The_lists

On 11/15/13 5:24 AM, Zeeshan Ali Shah wrote:

Hi,
I followed the guide from https://github.com/chapmanb/biocloudcentraland
managed to run locally, But only see AWS in combo box, How to add private
Openstack in it?

--

Regards

Zeeshan Ali Shah
System Administrator - PDC HPC
PhD researcher (IT security)
Kungliga Tekniska Hogskolan
+46 8 790 9115
http://www.pdc.kth.se/members/zashah


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Setting a queue for torque submission

[Jennifer Jackson]

Hello, I am going to move your question over to the 
galaxt-...@bx.psu.edu mailing list to give it better visibility to the 
development/local install community. 
http://wiki.galaxyproject.org/MailingLists#The_lists
I didn't find it over here already, but apologies if double posted. 
Also, since I don't know the best answer, will let others jump in!

Best,
Jen
Galaxy team


On 11/14/13 6:35 AM, Xian Su wrote:

Greetings

I'm having a hard time getting job submission to work via torque. 
Posted below is the relevant part of my universe file and job_conf.xml.


The main cause comes from our torque server requiring a queue to be 
requested. I can submit jobs just fine via job .sub files via command 
line using qsub -q M30


Running jobs via webgui results in the following:
galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28) 
pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all 
destinations
galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All 
attempts to submit job failed


On the torque server's pbs logs, I see the corresponding
11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply 
code=15039(No default queue specified MSG=requested queue not found), 
aux=0, type=QueueJob, from xians@podmt1-100-62.novalocal


In my universe_wsgi.ini, I'm currently using the settings:
start_job_runners = pbs
default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/
^I mainly have no idea how to find the correct syntax for this pbs:///

But when I comment out default_cluster_job_runner and instead 
uncomment the line for the following job conf, I get the same error:




load="galaxy.jobs.runners.local:LocalJobRunner"/>
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>








id="Resource_List">walltime=72:00:00,nodes=1:ppn=12

M30









Thank you in advance for any help.

Regards,
Xian


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

[Jennifer Jackson]

Hi Lindsay,

Nice to hear that Vipin's server worked out for you.

A reduction in the number of lines is completely expected. You should 
have the same number of lines in the BED12 file as you have unique "ID"s 
in the GFF3 file, if you want to double check. This is the same as the 
number of unique transcripts in any of the files, if summed up correctly.


Why is this? A GFF3 file has one line per feature. Part of an exon, etc. 
with further (this can vary) annotation that tells you if it is 5' UTR, 
or CDS, etc. When converting GFF3 -> BED12, all the features for a 
particular transcript are rolled up into a single line of output. 
Transcripts will have a unique "ID" by GFF3 specification - and all 
features that belong to that transcript will have it in the GFF3 file's 
attributes field (it is usually the first attribute listed).


When you converted just GFF3 -> BED6, each feature was individually 
converted into a distinct line of BED formatted output, there was no 
summing up to group the information for the transcript as a whole.


The Galaxy wiki has more - GFF3 can represent other kinds of data, and 
that is covered in the link-outs to the original spec, but this is the 
gist of the meaning for your specific data.


Glad I could help before, and that Vipin had the tool online & available 
to simplify things!


Best,

Jen
Galaxy team

On 11/12/13 4:12 PM, Lindsay Rutter wrote:

Hello Jennifer:

Thank you for your very helpful and detailed explanation!

I ended up using the site that Vipin provided in his message 
(https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed).


Indeed, it produced a file with 12 columns that appears to be in a 
reasonable bed format (including the 10th column being an integer, 
with the 11th and 12th column consisting of that integer number of 
items separated by commas).


However, I noticed that the number of lines in the file went 
from 183,748 (in the .gff3 file) to 11,506 (in the 12-column .bed file).


In your opinion, does this seem like a reasonable reduction in number 
of lines? I was not expecting that (in fact, I was expecting the 
number of lines would stay the same, as they did going from .gff3 to 
6-column .bed file), but I am quite inexperienced using these files.


Thanking you...
Lindsay




On Mon, Nov 11, 2013 at 11:15 AM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote:


Hello,

There are no tools directly on the public Galaxy site to transform
a GFF3 dataset into a BED12 dataset. However, the Tool Shed has a
repository called ' fml_gff3togtf' that includes a tool for this
purpose, for use in a local install. The description is a bit
bothersome in that it a slightly incorrect datatype statement, so
be sure to test out the results. (the word "wiggle" has no place
in this statement: "
gff3_to_bed_converter.py: This tool converts gene transcript annotation from 
GFF3 format to UCSC wiggle 12 column BED format.")
http://getgalaxy.org
http://usegalaxy.org/toolshed

I see your post at Biostar, and it might be helpful to let you
know what a BED12 file represents (plus I'll post this there, may
help others):
http://www.biostars.org/p/85869/

A BED12 file describes the complete, often spliced, alignment of a
sequence to a reference genome. This does not include minor base
variation, it is a macro alignment. You can think of each of the
blocks as being "exons", although there is no magic here - if the
sequence or genome had quality problems, or significant variation
(large insertion or deletion), that could cause the alignment to
fragment as well.
Here is the data description:
http://wiki.galaxyproject.org/Learn/Datatypes#Bed

To see examples, at UCSC (genome.ucsc.edu
<http://genome.ucsc.edu>), EST or mRNA track will have this as the
primary table format. All gene track can also be in BED12 format,
or in a related one, genePred:
http://genome.ucsc.edu/FAQ/FAQformat.html#format9

UCSC also has line-command utilities to convert between the
formats, pre-compiled versions are here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

Either way, you can convert the data, then load up into the public
Galaxy (usegalaxy.org <http://usegalaxy.org>) and proceed with
your analysis. BEDTools works well with BED12 files. There is
definitely information loss attempting to transform BED6 -> BED12,
as the global alignment is lost. And adjusting attributes such as
score or name are often a preference, so you can alter these
however you want, as long as the attribute formatting rules for
the columns are followed.

Hopefully this helps,

Jen
Galaxy team


On 11/9/13 3:29 PM, lrutter @iastate.edu <http://iastate.edu> wrote:

Hello Galaxy:

I am trying over

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

[Jennifer Jackson]

Hello,

There are no tools directly on the public Galaxy site to transform a 
GFF3 dataset into a BED12 dataset. However, the Tool Shed has a 
repository called ' fml_gff3togtf' that includes a tool for this 
purpose, for use in a local install. The description is a bit bothersome 
in that it a slightly incorrect datatype statement, so be sure to test 
out the results. (the word "wiggle" has no place in this statement: " 
gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.")

http://getgalaxy.org
http://usegalaxy.org/toolshed

I see your post at Biostar, and it might be helpful to let you know what 
a BED12 file represents (plus I'll post this there, may help others):

http://www.biostars.org/p/85869/

A BED12 file describes the complete, often spliced, alignment of a 
sequence to a reference genome. This does not include minor base 
variation, it is a macro alignment. You can think of each of the blocks 
as being "exons", although there is no magic here - if the sequence or 
genome had quality problems, or significant variation (large insertion 
or deletion), that could cause the alignment to fragment as well.

Here is the data description:
http://wiki.galaxyproject.org/Learn/Datatypes#Bed

To see examples, at UCSC (genome.ucsc.edu), EST or mRNA track will have 
this as the primary table format. All gene track can also be in BED12 
format, or in a related one, genePred:

http://genome.ucsc.edu/FAQ/FAQformat.html#format9

UCSC also has line-command utilities to convert between the formats, 
pre-compiled versions are here:

http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

Either way, you can convert the data, then load up into the public 
Galaxy (usegalaxy.org) and proceed with your analysis. BEDTools works 
well with BED12 files. There is definitely information loss attempting 
to transform BED6 -> BED12, as the global alignment is lost. And 
adjusting attributes such as score or name are often a preference, so 
you can alter these however you want, as long as the attribute 
formatting rules for the columns are followed.


Hopefully this helps,

Jen
Galaxy team


On 11/9/13 3:29 PM, lrutter @iastate.edu wrote:

Hello Galaxy:

I am trying overall to convert a .gff3 file to 12-column .bed file.

I first tried GFF-to-BED converter, but it gave a 6-column .bed file.

Then, I tried BED-to-bigBed converter by inputting the 6-column .bed 
file. I get an error "Unspecified genome build, click the pencil icon 
in the history item to set the genome build".


So, I click the pencil icon, and see 4 tabs at the top. I set the 
"Attributes" tab as in the attached image (Attributes.png).


But then, when I select "Convert Format", I am only seeing an option 
that outputs .bed12 file as "Convert Genomic Intervals to Strict 
BED12". I am a bit confused about this because I specified the input 
file as a .bed file (and not genomic intervals, unless I am 
misunderstanding something).


In any case, when I select "Convert Genomic Intervals to Strict 
BED12", I do get a .bed file with 12 columns. But I would like to ask 
if I may have lost information going from the .gff3 to .bed(6) to 
.bed(12)?


(I feel that scores were all set to "0" from .gff3 to .bed(6), and 
columns 10, 11, 12 (block counts, sizes, and starting positions) were 
all set to zero going from .bed(6) to .bed(12)).


If I am correct that there is information loss, is there a system in 
Galaxy to prevent this, and transfer as much information as possible 
from .gff3 to .bed(12)?


Thank you.
L. Rutter

** Below is a head of my three files (the species is P. dominula):

.gff3 file

##gff-version 3
##date Mon Nov  4 14:54:42 2013
##source gbrowse gbgff gff3 dumper
PdomScaf0001maker   gene15  1963.   - . 
Name=PdomGene00025;ID=1;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274
PdomScaf0001maker   mRNA15  1963.   - . 
Name=PdomMRNA00025.1;Parent=1;ID=2;_QI=216%7C0%7C0.2%7C0.6%7C0.5%7C0.6%7C5%7C0%7C98;_eAED=0.43;_AED=0.43;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274-mRNA-1
PdomScaf0001maker   exon15  100 -0.094  - .   
Parent=2;ID=3
PdomScaf0001maker   CDS 15  100 .   - 2   
Parent=2;ID=4
PdomScaf0001maker   exon223 300 21.8- .   
Parent=2;ID=5
PdomScaf0001maker   CDS 223 300 .   - 2   
Parent=2;ID=6
PdomScaf0001maker   exon717 765 22.4- .   
Parent=2;ID=7


.bed(6) file

PdomScaf000114  1963gene0   -
PdomScaf000114  1963mRNA0   -
PdomScaf000114  100 exon0   -
PdomScaf000114  100 CDS 0   -
PdomScaf0001222 300 exon0   -
PdomScaf0001222 300 CDS 0   -
PdomScaf0001716 765 exon0   -
PdomScaf0001716 765 CDS 0   -
PdomScaf0001906 947   

Re: [galaxy-dev] multiple output tool in workflow

[Jennifer Jackson]

Hi Fan,

The   block should contain one line for each of the 
output files. I believe that you need to name these differently. 
"output1", "output2", etc. Or you can add in text and use variables, if 
you add in the " label" option.


Others can correct or add to my comments.

Good luck!

Jen
Galaxy team

On 11/8/13 5:41 PM, Jun Fan wrote:


Hi Jen

 Thanks for your reply. Yes, it is my own tool.

The outputs element is







In the command element, the three output files are defined as below

$output 
/$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam 
/$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta


Is there anything wrong here?

Best regards!

Jun

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* 09 November 2013 01:05
*To:* Galaxy Dev
*Cc:* Jun Fan
*Subject:* multiple output tool in workflow

Hi Jun,

There is probably a problem with the tool design itself, but that may 
be what you are asking how to solve. I wouldn't think this is a 
problem with workflows at first pass.


Is this your own tool? Or a tool from the tool shed (the repo 
developer is usually the one to make changes, unless you want to try)?
This is the primary tool development wiki, the "  tag set" is 
where I would double check the tool first.

http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

I am moving this over to the galaxy-...@bx.psu.edu 
<mailto:galaxy-...@bx.psu.edu> mailing list since it is a tool 
development question.


Jen
Galaxy team

On 11/8/13 10:19 AM, Jun Fan wrote:

Hi all,

  I am trying to creating a workflow from history. One of the
tool used generates multiple outputs in the format of gff3, fasta
and sam. Gff3 will be visualized in IGV and the fasta file is
doing further BLAST analysis. Now the problem is that the
automatically generated workflow does not connect the
having-multiple-output tool and the BLAST tool. I failed even I
tried to connect these two tools in the workflow by hand. I am
guessing this is due to only the main output type (gff3) is
recognized in the workflow. How could I solve this problem?

Best regards and have a nice weekend!

Jun




___

The Galaxy User list should be used for the discussion of

Galaxy analysis and other features on the public server

at usegalaxy.org.  Please keep all replies on the list by

using "reply all" in your mail client.  For discussion of

local Galaxy instances and the Galaxy source code, please

use the Galaxy Development list:

  


   http://lists.bx.psu.edu/listinfo/galaxy-dev

  


To manage your subscriptions to this and other Galaxy lists,

please use the interface at:

  


   http://lists.bx.psu.edu/

  


To search Galaxy mailing lists use the unified search at:

  


   http://galaxyproject.org/search/mailinglists/



--
Jennifer Hillman-Jackson
http://galaxyproject.org


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] multiple output tool in workflow

[Jennifer Jackson]

Hi Jun,

There is probably a problem with the tool design itself, but that may be 
what you are asking how to solve. I wouldn't think this is a problem 
with workflows at first pass.


Is this your own tool? Or a tool from the tool shed (the repo developer 
is usually the one to make changes, unless you want to try)?
This is the primary tool development wiki, the "  tag set" is 
where I would double check the tool first.

http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

I am moving this over to the galaxy-...@bx.psu.edu mailing list since it 
is a tool development question.


Jen
Galaxy team


On 11/8/13 10:19 AM, Jun Fan wrote:


Hi all,

  I am trying to creating a workflow from history. One of the tool 
used generates multiple outputs in the format of gff3, fasta and sam. 
Gff3 will be visualized in IGV and the fasta file is doing further 
BLAST analysis. Now the problem is that the automatically generated 
workflow does not connect the having-multiple-output tool and the 
BLAST tool. I failed even I tried to connect these two tools in the 
workflow by hand. I am guessing this is due to only the main output 
type (gff3) is recognized in the workflow. How could I solve this problem?


Best regards and have a nice weekend!

Jun



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Bowtie2 mm9 index

[Jennifer Jackson]

Hi Mary,

The data was restored this morning. Good luck with the new run,

Jen
Galaxy team


On 11/7/13 2:57 PM, Jennifer Jackson wrote:

Hello Mary,

The underlying data is not complete for all mm9 reference genomes for 
the Bowtie2/Tophat2 tools, causing the error. It is a known issue and 
we expect to have it corrected very soon now. We consider this 
important and high priority, our apologies for the confusion it caused.


A list of known data issues since the migration of usegalaxy.org are 
listed in this ticket. You can follow the ticket to find out when this 
genome has been restored: https://trello.com/c/SbizUDQt


Best,

Jen
Galaxy team

On 10/29/13 7:43 AM, Davis, Mary wrote:


Greetings---

I tried to run an alignment using Bowtie2 and got this message-

format: bam, database: mm9

Could not locate a Bowtie index corresponding to basename 
"/galaxy/data/mm9/mm9canon/bowtie2_index/mm9canon" Error: Encountered 
internal Bowtie 2 exception (#1) Command: 
/galaxy/software/linux2.6-x86_64/pkg/bowtie2-2.1.0/bin/bowtie2-align 
--wrapper basic


I imported Illumina fastq data, groomed them, and then did the 
analysis using the built-in index mouse, both full and male, and had 
the same error message.


I'm relatively new to this, and don't see what I missed.

Thanks

Mary E. Davis, Ph.D.

Professor

Department of Physiology & Pharmacology

West Virginia University Health Sciences Center

PO Box 9229

Morgantown, WV  26506-9229



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Empty bowtie2 output

[Jennifer Jackson]

Hello,

The mm9 bt2 indexes were restored this morning. You can track this and 
other current data fixes through this Trello card:

https://trello.com/c/SbizUDQt

Thanks for your patience during the migration. We are moving on to data 
now, both corrections and updates.


Jen
Galaxy team

On 11/7/13 3:58 PM, IIHG Galaxy Administrator wrote:

Sending to galaxy-dev instead.

From: Srinivas Maddhi >

Date: Friday, November 1, 2013 11:56 AM
To: "galaxy-u...@lists.bx.psu.edu 
" >

Subject: Empty bowtie2 output

In follow-up to 
http://user.list.galaxyproject.org/Empty-bowtie2-output-tp4656137.html, is 
there:
- an ETA on when the issue with Bowtie2, in August 2013 distribution, 
generating empty output will be fixed (if not already fixed) ?
- a suggested workaround (revert to an older version of that 
particular tool etc.) in the meantime ?


Thank you.

Unrelated: wasn't able to determine how to update that thread to 
request status, hence creating a new one.




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Contributing to genome indexes on rsync server

[Jennifer Jackson]

Thanks,

There have been no public data updates since the migration started (late 
last spring we froze the data). But there are some known issues and data 
that is ready to be released, in the process of becoming ready, etc. We 
expect to be able to start working on this again in the very near term.


To start this off, the mm9 bowtie2 indexes were restored this morning:
https://trello.com/c/SbizUDQt

And these other finds are great, thanks Bjoern. I will add them to the 
public card. A few errors that were corrected later last spring popped 
out again, but will also be fixed. Small, but will be addressed ASAP.


Adding in any missing .2bit files in general are on our internal to-do 
list. Older genomes have other inconsistencies that will be addressed. 
The goal is to have the data filled in with complete indexes around the 
end of Nov, then filled in with newly released genomes/more variants for 
important model organisms by the end of the year. All of this depends on 
various factors, but this is where we are shooting for.


Thanks and if anything else off is noted, please feel free to send to 
the list or add to the card. All input is welcome - we want this to be a 
great resource for everyone - time to get back to making that happen now 
that the migration is wrapping up!


Jen
Galaxy team

On 11/8/13 2:00 AM, Bjoern Gruening wrote:

Hi,

to chime into this discussion.

I found some inconsistency during my rsync endeavor and I'm curious if 
there is any way to contribute to that service.


--
xenTro3 xenTro3 Frog (Xenopus tropicalis): xenTro3 
/galaxy/data/xenTro3/seq/xenTro3.fa

but only
/xenTro3.fa.gz exists.
---
ce6 /data/0/ref_genomes/ce6/ce6.2bit is missing from twobit.loc
---
ce6 has no .fa file under seq/ but in allfasta.loc there is a 
reference to it ce6 Caenorhabditis elegans: ce6 
/galaxy/data/ce6/seq/ce6.fa

---
TAIR9 and TAIR10 is not available via rync
---
Bowtie2 indices are missing for ce6, xentTro3


Thanks,
Bjoern


Hi Jennifer,

Today I was trying to pull some bowtie2 indices from Galaxy rsync server for 
PhiX to run some tests and just got the ones for bowtie1… I'm wondering what's 
the state in regards to this past thread and what we can do to help in here.

Cheers!
Roman

7 mar 2013 kl. 20:01 skrev Jennifer Jackson mailto:j...@bx.psu.edu>>:

> Hi Brad (and Roman),
>
> The team has talked about this in detail. There are a few wrinkles with just 
pulling in indexes - Dan is doing some work that could change this later on, but 
for now, the rsync will continue to point to the same location as Main's genome 
data source. This means that there are some limits on what we can do immediately. 
Setting up a submission pipe is one of them - there just isn't resource to do this 
right now or a common place distinct from Main to house the data. A few other 
ideas came up - we can chat later, each had side issues.
>
> But I saw your tweet and think that it is great that you are pulling 
CloudBioLinux data from the rsync now, so let's get as much data in common as 
possible, so you have data to work with near term.
>
> I am in the process of adding bt2 indexes - some are published to Main/rsync 
server already and some are not, but more will show up over the next week or so 
(along with more genomes and other indexes). I'll take a look at what you have and 
pull/match what I can. Genome sort order and variants are my concerns, both 
require special handling in processing and .locs. If it takes longer to check, I 
am just going to create here if I haven't already. The GATK-sort hg19 canonical is 
already on my list - it needed all indexes, not just bw2. When the next 
distribution goes out, I'll list what is new on the rsync in the News Brief.
>
> For the Novoalign indexes, I'm not quite sure what to do about those yet. Or 
for any indexes associated with tools or genomes not hosted on Main. Do you want 
to open a card for those and any other cases that are similar? We can discuss a 
strategy from there, maybe at IUC, if Greg/Dan thinks it is appropriate. Please 
add me so I can follow.
>
> I'll be in touch as I go through the data. Thanks for your patience on this!
>
> Jen
> Galaxy team
>
> On 2/21/13 12:43 PM, Brad Chapman wrote:
>> Hi all;
>> Is there a way for community members to contribute indexes to the rsync
>> server? This resource is awesome and I'm working on migrating the
>> CloudBioLinux retrieval scripts to use this instead of the custom S3
>> buckets we'd set up previously:
>>
>>https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/biodata/galaxy.py
>>
>> It's great to have this as a public shared resource and I'd like to be
>> able to contribute back. From an initial pass, here are the things I'd
>> like to do:
>>
>> - Include bowtie2 indexes for more ge

Re: [galaxy-dev] Bowtie2 mm9 index

[Jennifer Jackson]

Hello Mary,

The underlying data is not complete for all mm9 reference genomes for 
the Bowtie2/Tophat2 tools, causing the error. It is a known issue and we 
expect to have it corrected very soon now. We consider this important 
and high priority, our apologies for the confusion it caused.


A list of known data issues since the migration of usegalaxy.org are 
listed in this ticket. You can follow the ticket to find out when this 
genome has been restored: https://trello.com/c/SbizUDQt


Best,

Jen
Galaxy team

On 10/29/13 7:43 AM, Davis, Mary wrote:


Greetings---

I tried to run an alignment using Bowtie2 and got this message-

format: bam, database: mm9

Could not locate a Bowtie index corresponding to basename 
"/galaxy/data/mm9/mm9canon/bowtie2_index/mm9canon" Error: Encountered 
internal Bowtie 2 exception (#1) Command: 
/galaxy/software/linux2.6-x86_64/pkg/bowtie2-2.1.0/bin/bowtie2-align 
--wrapper basic


I imported Illumina fastq data, groomed them, and then did the 
analysis using the built-in index mouse, both full and male, and had 
the same error message.


I'm relatively new to this, and don't see what I missed.

Thanks

Mary E. Davis, Ph.D.

Professor

Department of Physiology & Pharmacology

West Virginia University Health Sciences Center

PO Box 9229

Morgantown, WV  26506-9229



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

[Jennifer Jackson]

Hi Curtis,
This is still open but I expect to correct this very soon, along with 
new data additions (but corrections first on the list!). We definately 
consider this important and apologize that this has impacted your 
paper's supplemental creation.


There is a Trello ticket containing the known data problems since the 
migration of usegalaxy.org, you can follow for updates here: 
https://trello.com/c/SbizUDQt


Thanks!

Jen
Galaxy team

On 10/29/13 8:18 AM, Curtis Hendrickson (Campus) wrote:


Jennifer,

What's the status of bowtie2/mm9 index on PSU main?

When I select tophat2, it offers me mm9 as a choice for built-in indexes.

However, when the job runs, I get the following error, indicating the 
bowtie2/mm9 indexes are missing (below).


Any insight into whether this is expected, or what the ETA is until 
the index would be installed, would be great.


I'm trying to reproduce work on PSU I ran on my local galaxy, so that 
we can link to it for supplemental materials for a paper.


Thanks,

Curtis

PS -- I clicked the submit bug button a few days ago, but haven't 
received a response yet.


Fatal error: Tool execution failed

[2013-10-29 10:13:27] Beginning TopHat run (v2.0.9)

---

[2013-10-29 10:13:27] Checking for Bowtie

   Bowtie version: 2.1.0.0

[2013-10-29 10:13:27] Checking for Samtools

 Samtools version: 0.1.18.0

[2013-10-29 10:13:27] Checking for Bowtie index files (genome)..

Error: Could not find Bowtie 2 index files 
(/galaxy/data/mm9/mm9full/bowtie2_index/mm9full.*.bt2)


*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Friday, September 20, 2013 4:00 PM
*To:* Curtis Hendrickson (Campus)
*Subject:* Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

Thanks Curtis,

I am actually working to try to get mm9 out there right now. No 
promises, but is just one (well, three, including variants)! If 
technical is a go, then will do it. Ideally others soonish. We'll see.


The last news brief has help for the Data manager, it may be that you 
need to do some config changes to get it going. I am certainly no 
expert - this is Dan's and under active development - but is where I 
would start.


Jen

On 9/20/13 1:25 PM, Curtis Hendrickson (Campus) wrote:

Thanks for the rapid reply! I have some questions and comments,
but need to read up on Data Managers (that admin page seems
non-functional in our local galaxy, despite being on latest code)
first.

    Regards,

Curtis

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Friday, September 20, 2013 2:34 PM
*To:* Curtis Hendrickson (Campus)
*Cc:* galaxy-...@bx.psu.edu <mailto:galaxy-...@bx.psu.edu>
*Subject:* Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

Hello Curtis,

The datacache was originally pointed to the data staging area and
is now pointed to the data published area. The difference is that
the published area contains data and location (.loc) files that
are in synch and have completed final testing. It is your choice
about whether to use the staged-only data - it depends how risk
tolerant your project is and if you plan on testing. But, that
said, I think it is almost certainly fine or our team wouldn't
have staged it yet. A vanishingly small number of datasets are
pulled back once they make it to staging, and this is why we were
comfortable pointing datacache there in the first place (were
unable to point to the published area at first, but wanted to make
the data available ASAP).

Going forward - I can let you know that these indexes are very
easy to create: one command-line execution, then add one line to
the associated .loc file. Instructions are here, see "Bowtie and
Tophat":
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

For one or few genomes, not a problem. For hundreds of genomes
with variants, can become tedious even with helper tools and in
our case, the processing interacted with disk that was undergoing
changes (as we have been working on system configuration most of
the summer). Also, with the Data Manager is now available,
creating batch indexes for use via rsync become lower priority.
Even so, I would expect more indexes to be fully published once
the final configuration is in place, as many are already staged or
close being staged (watch the yellow banner on Main).

Hopefully this helps to explain the data, guides you to making an
informed decision, and aids with creating your own indexes as needed,

Thanks!
Jen
Galaxy team



On 9/18/13 1:04 PM, Curtis Hendrickson (Campus) wrote:

Folks,

First, I wanted to thank you for making the datacache
available
(http://wiki.galaxyproject.org/Admin/Data%20Integration;
rsync://datacache.g2.bx.psu.edu). It's 

[galaxy-dev] Nov 04, 2013 Galaxy Distribution

[Jennifer Jackson]

Nov 04, 2013 Galaxy Distribution 



*usegalaxy.org*
*CompleteNews Brief 
*


*Highlights:*

 *

   A/*security vulnerability*/with filter tools trapped and
   fixed:*Upgrade or Patch NOW
   *

 *

   Galaxy Tool Migration:48 tools migrated to Tool Shed
   
for
   a leaner distribution.

 *

   Improvedtools for administrators
   (email
   verification, reports).

 *

   The framework forTools
   ,Visualizations
   ,
   and theCore
   have
   been upgraded for performance and scalability.

 *

   Come see! A whopping26 pull requests incorporated
   
!.
   Many thanks to our open source community!

 *

   NumerousTool Shed enhancements and upgrades
   :
   Api,READMEs, Functional Tests, easier installs, and much much more.

 *

   Plus enhancements toWorkflows
   ,API
   ,CloudLaunch
   ,UI
   , andBug
   Fixes
   .

http://getgalaxy.org 

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org 


new:   $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade:   $ hg pull
   $ hg update release_2013.11.04

/Thanks for using Galaxy!/

The Galaxy Team 

Posted to theGalaxy News on 2013-11-04
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] Inquiring

[Jennifer Jackson]

Hi Yan,

I do not know for 100% certain, but Hans gave advice recommending this 
and I trust his skill in this area greatly. It is certainly worth a try. 
If you have trouble, just write back in with details and be sure to stay 
on the galaxy-dev list as you are doing. This is where the core 
experience with running large local installs is concentrated.


It is a holiday here in the US starting around now into early evening 
for those of us with small kids (Halloween) - so you may see some 
question delays for a few hours - many do this all before dark now 
(safer). But we'll BE BACK! :)


Jen
Galaxy team


On 10/31/13 12:54 PM, Yan Luo wrote:

Dear Jen,

Thanks. Could you please let me know if we only need change the IP 
address of file "universe_wsgi.ini"? Then we can login by the new IP 
address. Is it?


Best Wishes,

Yan


On Thu, Oct 31, 2013 at 3:45 PM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote:


Yan,

The *universe_wsgi.ini* file is at the very top level of the
galaxy install. This is the same directory location where you
start the server.

Hopefully you have found it!

Jen
Galaxy team


On 10/31/13 10:52 AM, Yan Luo wrote:

Hi, Hans-Rudolf,

Thanks for your response. We didn't build a new server, we just
plan to change the IP address of the old server (The server will
automatically get a new IP address when the physical address is
moved). When server is started with new IP address, can we login
directly using new IP address from client (web browser)? Could
you please let me know if we only need change the IP address of
file "universe_wsgi.ini"? Where is this file?

Best Wishes,

Yan Luo, Ph.D.
Rockville, MD


On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Yan

Assuming you have copied everything to the new server and you
have changed the "host = xxx.xxx.xxx.xxx" line in the
'universe_wsgi.ini' file it should all work

Regards, Hans-Rudolf



On 10/31/2013 04:36 PM, Yan Luo wrote:

Dear All,

We have a question regarding the Galaxy server. We
installed a local
version on our Linux machine and need move to a new
place. The IP
address will be changed. Could you please let me know if
the server can
be still used? I mean, we can use the new IP to open the
home page of
Galaxy and use it. For example if the new IP is
"xxx.xxx.xxx.xxx", which
is similar as before(I just replace the IP address). Do
we need reset
anything for Galaxy? Will the Galaxy use the fixed IP
address in the
system when it was installed?

xxx.xxx.xxx.xxx:8080/root

Looking forward to hearing from you.

Best Wishes,

Yan


On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor
mailto:n...@bx.psu.edu>
<mailto:n...@bx.psu.edu <mailto:n...@bx.psu.edu>>> wrote:

Hi Yan,

I've moved this discussion to the galaxy-dev list
since it pertains to a
local installation of Galaxy.

Responses to your questions follow, in-line.

Yan Luo wrote:
 > Dear Sir,
 >
 > (1)We installed Galaxy, but recently the user
can't registered
and got the
 > following error, how can we fix it?
 >
 > Sever error
 > An error occurred. See the error logs for more
information.(To
turn debug on
 > to display ...).

Since debug = False in universe_wsgi.ini, you should
be able to find a
more detailed error message in the log file.  If
starting Galaxy with:

   % sh run.sh --daemon

The default log file is 'paster.log' in Galaxy's root
directory.

 > (2) Could you please let me know if there is any
command to stop
galaxy?

If starting with the --daemon flag (as above), you
can use:

   % sh run.sh --stop-daemon

If running in the foreground, you can use Ctrl-C to
terminate the
process.  There is a recent bug whereby Ctrl-C is
ineffective on some
platforms under Python 2.6 - in this case you will
have to kill/pkill
the process manually.  We are working on a fix for
the latter.

 > (3) If I reset universe_wsgi.ini file

Re: [galaxy-dev] [galaxy-user] Inquiring

[Jennifer Jackson]

Yan,

The *universe_wsgi.ini* file is at the very top level of the galaxy 
install. This is the same directory location where you start the server.


Hopefully you have found it!

Jen
Galaxy team

On 10/31/13 10:52 AM, Yan Luo wrote:

Hi, Hans-Rudolf,

Thanks for your response. We didn't build a new server, we just plan 
to change the IP address of the old server (The server will 
automatically get a new IP address when the physical address is 
moved). When server is started with new IP address, can we login 
directly using new IP address from client (web browser)? Could you 
please let me know if we only need change the IP address of file 
"universe_wsgi.ini"? Where is this file?


Best Wishes,

Yan Luo, Ph.D.
Rockville, MD


On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz > wrote:


Hi Yan

Assuming you have copied everything to the new server and you have
changed the "host = xxx.xxx.xxx.xxx" line in the
'universe_wsgi.ini' file it should all work

Regards, Hans-Rudolf



On 10/31/2013 04:36 PM, Yan Luo wrote:

Dear All,

We have a question regarding the Galaxy server. We installed a
local
version on our Linux machine and need move to a new place. The IP
address will be changed. Could you please let me know if the
server can
be still used? I mean, we can use the new IP to open the home
page of
Galaxy and use it. For example if the new IP is
"xxx.xxx.xxx.xxx", which
is similar as before(I just replace the IP address). Do we
need reset
anything for Galaxy? Will the Galaxy use the fixed IP address
in the
system when it was installed?

xxx.xxx.xxx.xxx:8080/root

Looking forward to hearing from you.

Best Wishes,

Yan


On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor mailto:n...@bx.psu.edu>
>> wrote:

Hi Yan,

I've moved this discussion to the galaxy-dev list since it
pertains to a
local installation of Galaxy.

Responses to your questions follow, in-line.

Yan Luo wrote:
 > Dear Sir,
 >
 > (1)We installed Galaxy, but recently the user can't
registered
and got the
 > following error, how can we fix it?
 >
 > Sever error
 > An error occurred. See the error logs for more
information.(To
turn debug on
 > to display ...).

Since debug = False in universe_wsgi.ini, you should be
able to find a
more detailed error message in the log file.  If starting
Galaxy with:

   % sh run.sh --daemon

The default log file is 'paster.log' in Galaxy's root
directory.

 > (2) Could you please let me know if there is any
command to stop
galaxy?

If starting with the --daemon flag (as above), you can use:

   % sh run.sh --stop-daemon

If running in the foreground, you can use Ctrl-C to
terminate the
process.  There is a recent bug whereby Ctrl-C is
ineffective on some
platforms under Python 2.6 - in this case you will have to
kill/pkill
the process manually.  We are working on a fix for the latter.

 > (3) If I reset universe_wsgi.ini file and want to set an
administrator
 > user(I can add a line in the above file), how can I get the
password? Should
 > I stop galaxy(See question 2) first? then run
"./setup.sh" and
"./run.sh".

setup.sh would have only been necessary prior to running
Galaxy the
first time, however, this step has recently been removed.
 If you are
referencing documentation that still refers to setup.sh,
please let us
know so we can update it - I did notice this was still on the
"Production Server" page, so I removed it from there.

You no longer need to run setup.sh at all.

 > (4) If I run "setup.sh", will a new file
"universe_wsgi.ini" be
generated?
 > if I want to change this file,should I edit it before
"run.sh"
and after
 > "setup.sh". Is it right?

setup.sh and its replacements in run.sh and the Galaxy
application
itself never overwrite files, they only create files from
sample files
if they do not exist.

 > (5) I read some of your docs, command "sh setup.sh"(sh
run.sh) and
 > "./setup.sh"(./run.sh), which one is correct under Linux?

Both syntaxes are effectively the same in most cases.

--nate

 

[galaxy-dev] Tool XML form building bug with ?

[Jennifer Jackson]

Moving this over to galaxy-...@bx.psu.edu, the best list for tool design 
questions. Best! Jen, Galaxy team


On 10/30/13 2:24 PM, dam...@learningpoint.ca wrote:
Has anyone run into this?  I'm building a general-purpose filter 
control on my galaxy tool xml template for enabling numeric fields to 
be filtered by > < etc. parameters - in a user friendly way.  I have a 
select list  driven by a data table:

...
  

  
...
This works fine in building a list of fields to select from.  Then I add
  
  

but nothing happens, sort remains incorrect and no extra value.  I try 
these same filters on a previous  in form that is driven 
by  and they work fine.


I also tried applying  to no avail on 
from_data_table options tag, but from from_file options, no problem.


So I start to think there's a bug whereby NO filters work on from_data_table="bccdc_blast_fields" /> input?  I've surveyed the 
galaxy.tools.parameters.dynamic_options
python code, but can't see a decision point there in which 
from_data_table work vs from_file choice is made; is it in another 
script file?


I'm using a BioLinux 2012 install that includes Galaxy.

Help appreciated!

Regards,

Damion Dooley
BC Centre for Disease Control
Vancouver, BC


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

Lei Yan,

I am very glad that this worked out! It looks like you have already 
helped at least one other user and I am sure others to come!


We were discussing this internally while you were working. Updates to 
the ready-loaded data on cloud instances will be getting a make-over in 
the near term (this has been in planning for a while). Ease of data 
install for locals is included in the larger project goals. Technical 
implementation details are being sorted out to ensure the most robust 
solution, but data services that meet our project's three core goals of 
"accessible, reproducible, and transparent" are without question the 
central design criteria for success.


Thank you again! We very much value the patience, tenacity, and time you 
took to not only see this through for yourself, but to post your 
experience & methods back to the list so clearly to share with others. 
Our community, most definitely including you, are so important. We are 
all "Galaxy team" :)


Jen
Galaxy team


Hope this can help somebody.


Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Can not find hg_g1k_v37.fa.

[Jennifer Jackson]

Update:

We are hosting .2bit files as a standard on the rsync server, so this is 
how to retrieve sequence data. No .fa files will be served.


The advantages are that the files are 25% smaller, the rsyncs are 
quicker, and local/cloud users can easily convert to fasta format anytime.


I will be adding in these notes to our rsync wiki to avoid confusion 
going forward.


Thanks Shenwiyn, I am sure that this helped many other readers.

Jen
Galaxy team

On 10/16/13 12:39 PM, Jennifer Jackson wrote:

Hello Shenwiyn,

We can confirm that the hg_g1k_v37.fa is currently unavailable. We are 
working to correct this.


Meanwhile, the hg_g1k_v37.2bit files is available. This can be convert 
to fasta using the tool "twoBitToFa" available from UCSC in the 
downloads area, under source code, pre-compiled for several platforms: 
http://genome.ucsc.edu


You will likely want both files version anyway, as several tools rely 
on the .2bit file for input/reference.


Very sorry for the current inconvenience,

Jen
Galaxy team


On 9/4/13 7:03 PM, shenwiyn wrote:

Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find 
this data.When I use the command :
rsync -avzP 
rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa

the error occurred:
receiving incremental file list
rsync: link_stat "/hg_g1k_v37/seq/hg_g1k_v37.fa" (in indexes) failed: 
No such file or directory (2)

sent 4 bytes  received 6 bytes  4.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous 
errors) (code 23) at main.c(1532) [receiver=3.0.6]


Please any suggestions would be most welcome.

Thanks.


shenwiyn


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

  
  
Hi Lei,

You can download all at once or in two parts (for slower
connections):



iGenomes has been pretty good about using the exact same build as
released by the source with no changes for the GTF files, but I do
not know about the indexes - so do a test run once in place. Just to
let you know, creating these may be easier than downloading, is just
a single line command and you have a server to run this on, but the
choice is yours.

Jen
Galaxy team


On 10/16/13 1:11 PM, Lei Yan wrote:


  
Hi James,


I found this: http://bowtie-bio.sourceforge.net/manual.shtml
There are some Pre-built indexes in the right side of this
  page.
If I just need an hg19 index for colorspace, which index
  file can work for us?
Thanks again.


  
  

  Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



On Wed, Oct 16, 2013 at 2:54 PM, Lei
  Yan <leiyan2...@gmail.com>
  wrote:
  

  Hi Jen and James,
  
  
  Thanks for your info.
  Yes, we are already running a cloud instance (http://galaxyclass.genenetwork.org/).
  So if I can build the index for colorspace, then how
to configure it?
  And I didn’t find the “tophat_indexes_color” record
in the Admin - “View data tables registry”. Please see
attachment.
  
  


  

  Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center



  
  

  On Wed, Oct 16, 2013 at 2:35
PM, James Taylor <ja...@jamestaylor.org>
wrote:

  They are already running a local instance.
  
  I didn't realize that bowtie required a different
  index for colorspace
  alignment. So Lei, you will have to build the
  index using bowtie-build
  -C.
  
--
James Taylor, Associate Professor, Biology/CS,
Emory University


  
  
On Wed, Oct 16, 2013 at 3:31 PM, Jennifer
      Jackson <j...@bx.psu.edu>
  wrote:
  > Hello Lei,
  >
  > If genomes are not listed, that means
  that they are not indexed for use with
  > the tool. The test server is primarily
  for demonstration or test use
  > besides, and there could be other
  unexpected issues even if genomes are
  > listed (we really do test here). Also,
  the quotas are very small (10G). If
  > you want to use this tool, a local,
  cloud, or slipstream Galaxy is
  > recommended. Full choices with details
  are listed here:
  > http://wiki.galaxyproject.org/BigPicture/Choices
  > http://usegalaxy.org/toolshed
  >
  > Help for setup is here, with the galaxy-...@bx.psu.edu
  mailing list
  > available for further support. Tools will
  need to be installed, and indexes
  > created. You can rsync the genome, but
  most genomes will not have loc file
  > entries and indexes for SOLiD already
  created - see the Tophat manual for
  > the command to create these:
  > http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
  > http://wiki.galaxyproject.org/Admin/Data%20Integration
  > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
  >
  > Hopefully this helps!
 

Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy

[Jennifer Jackson]

Hello Lei,

These can go in the "bowtie_indices_color.loc" file. In fact, you don't 
need the "tophat_indexes" file as far as I know, those lines can be 
merged with what is in "bowtie_indexes". Both Bowtie and Tophat use the 
same indexes - one set for regular, one set for color. Then, both 
Bowtie2 and Tophat2 use the same indexes - only one type, no option for 
color. This structure is explained in more detail in the data link I 
sent and you can see examples in our rsync server's location files.


Jeremy/James - please correct me if I have any of this incorrect for 
their particular install. The above are the standard config instructions.


Thanks!
Jen
Galaxy team



On 10/16/13 12:54 PM, Lei Yan wrote:

Hi Jen and James,

Thanks for your info.
Yes, we are already running a cloud instance 
(http://galaxyclass.genenetwork.org/).

So if I can build the index for colorspace, then how to configure it?
And I didn’t find the “tophat_indexes_color” record in the Admin - 
“View data tables registry”. Please see attachment.



Lei Yan
Center for Integrative and Translational Genomics
The University of Tennessee Health Science Center


On Wed, Oct 16, 2013 at 2:35 PM, James Taylor <mailto:ja...@jamestaylor.org>> wrote:


They are already running a local instance.

I didn't realize that bowtie required a different index for colorspace
alignment. So Lei, you will have to build the index using bowtie-build
-C.

--
James Taylor, Associate Professor, Biology/CS, Emory University


On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:
> Hello Lei,
>
> If genomes are not listed, that means that they are not indexed
for use with
> the tool. The test server is primarily for demonstration or test use
> besides, and there could be other unexpected issues even if
genomes are
> listed (we really do test here). Also, the quotas are very small
(10G). If
> you want to use this tool, a local, cloud, or slipstream Galaxy is
> recommended. Full choices with details are listed here:
> http://wiki.galaxyproject.org/BigPicture/Choices
> http://usegalaxy.org/toolshed
>
> Help for setup is here, with the galaxy-...@bx.psu.edu
<mailto:galaxy-...@bx.psu.edu> mailing list
> available for further support. Tools will need to be installed,
and indexes
> created. You can rsync the genome, but most genomes will not
have loc file
> entries and indexes for SOLiD already created - see the Tophat
manual for
> the command to create these:
>

http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
> http://wiki.galaxyproject.org/Admin/Data%20Integration
> http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
>
> Hopefully this helps!
>
> Jen
> Galaxy team
>
>
> On 10/16/13 11:57 AM, Lei Yan wrote:
>>
>> Hi all,
>>
>> We are trying to use “Tophat for SOLiD”.
>> But this tool (Tophat for SOLiD) does not seem to be linked to the
>> reference genomes that are installed. I can see those genomes
on the Tophat
>> for illumina tool and the other tools that require a reference
genome.
>> Please see attachments.
>> Does anybody have any ideas for this? Thanks a lot.
>>
>>
>> Lei Yan
>> Center for Integrative and Translational Genomics
>> The University of Tennessee Health Science Center
>
>
> --
> Jennifer Hillman-Jackson
> http://galaxyproject.org
>




--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Can not find hg_g1k_v37.fa.

[Jennifer Jackson]

Hello Shenwiyn,

We can confirm that the hg_g1k_v37.fa is currently unavailable. We are 
working to correct this.


Meanwhile, the hg_g1k_v37.2bit files is available. This can be convert 
to fasta using the tool "twoBitToFa" available from UCSC in the 
downloads area, under source code, pre-compiled for several platforms: 
http://genome.ucsc.edu


You will likely want both files version anyway, as several tools rely on 
the .2bit file for input/reference.


Very sorry for the current inconvenience,

Jen
Galaxy team


On 9/4/13 7:03 PM, shenwiyn wrote:

Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find 
this data.When I use the command :
rsync -avzP 
rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa

the error occurred:
receiving incremental file list
rsync: link_stat "/hg_g1k_v37/seq/hg_g1k_v37.fa" (in indexes) failed: 
No such file or directory (2)

sent 4 bytes  received 6 bytes  4.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous 
errors) (code 23) at main.c(1532) [receiver=3.0.6]


Please any suggestions would be most welcome.

Thanks.


shenwiyn


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Consistently denied server access

[Jennifer Jackson]

Hi Rhea,

Are you using the new server address? This is noted on the upload form: 
"usegalaxy.org"


We will be updating the screencasts and such soon, there are other small 
changes that will go along with this one and we want to capture it all 
in one place. Meanwhile, I'll try to make this more obvious in the 
current wiki.


Good question, I am sure others will read and benefit from it!

If your problem is occurring with the new address, please let us know.

Take care,

Jen
Galaxy team

On 10/14/13 11:23 AM, Rhea Datta wrote:

Hello,

My account is under rrdatta@gmail.com .

I have been able to successfully transfer files and performed FTP 
uploads using Filezilla in the past. However in the last few days I 
have been consistently denied server access. The report I get is:


Status:Connection attempt failed with "ECONNREFUSED - Connection 
refused by server".


Please let me know if you have a solution to this problem.
Thank you so much
Rhea


--
*Rhea R Datta, PhD*
Postdoctoral Associate
New York University
r...@nyu.edu 
rrdatta@gmail.com 
(917) 613 4719


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Solenopsis invicta genome

[Jennifer Jackson]

Hi Patrick,

I think this is worth consideringand will run by team. Genomes are a bit 
on hold right now due to the move of the public server, but once that 
resumes, I have a ticket going with public requests in it. Would you 
please send me the details for this organism: exact accession(s), 
special build names/links, and such. You can send to me direct.
This is the ticket I'll be adding the info to, please don't add 
yourself, this is just so you can follow:

https://trello.com/c/kzVklAIE
(There is much more data in pipe, including genomes, tracked elsewhere).

Meanwhile, you don't need to wait (or want to!), to use the genome right 
now, do this as a _custom reference genome_ with tools. All you need is 
a fasta copy of the genome in your history. Pay attention to the 
"chromosome" identifiers and any identifiers in related GTF/BED files 
you intend to incorporate into your analysis - these almost without 
exception have to be /exactly the same /to function in downstream tool. 
Here's the how-to:

http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://vimeo.com/galaxyproject/customgenome
Note that the FTP server is now: "usegalaxy.org" instead of any server 
mentioned in the films, as noted on the "Upload Data" tool form.


Thanks,

Jen
Galaxy team



On 10/11/13 5:40 AM, patrick.j...@unil.ch wrote:

Hello,

I'm working in the university of Lausanne. We are currently working 
with fire ants, Solenopsis invicta.
I was wondering if that would possible to upload Solenopsis invicta's 
genome on the Galaxy platform, which could be very useful to us and

certainly to other people.

Thank you !

Patrick Joye


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Trouble viewing History from a particular laptop

[Jennifer Jackson]

Hi Olivia,

Our development team suggests checking the paster.log, plus, if 
applicable, proxy server logs.


From what we know, this kind of issue generally indicate a firewall 
issue, but without more information, it is difficult to diagnose.


Please keep replies on this mailing list instead (is the one for local 
install questions).


Thanks!

Jen
Galaxy team

On 10/9/13 2:31 PM, Olivia Choudhury wrote:

Hello,

I am a graduate student in the University of Notre Dame. I have 
installed a personal instance of Galaxy and have been developing tools 
there as a part of my research.


Everything worked well on my laptop until recently, when I could not 
view the 'History' panel, no matter which browser (Firefox, Chrome, 
Safari) I used on my laptop (Windows 7 OS). Everything works 
absolutely fine and I can view 'History' when I am using a desktop or 
any other laptop.


I have checked this across different operating systems and also 
ensured that no changes were made with the Firewall setup of my laptop.


I have attached a print screen of what the Galaxy page looks like.

It would be great if I could get some help with this.


Thanks a lot in advance,
Olivia


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] 2 RNAseq files in Main queue 1 week to map w/Top hat

[Jennifer Jackson]

Hi Theresa,

The clusters have been on and off for most of the last few weeks. The 
updated server is now up and much faster! We are actively seeking feedback.


If a job did end up failing due to a cluster or fileserver issue during 
the move, then please just re-run it. There could be many contributing 
factors and that system is no longer in use.


If jobs started now fail, from about two hours ago forward, then please 
submit as a bug report. New jobs are on the new cluster/server site and 
we definitely need to work out any issues. Help doing that is very much 
appreciated!


This is still relevant advice:
http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute
But, if you have grey jobs that are really two weeks old still, that 
would be very strange and we would want to fix it. Would you please 
share a history with me?

http://wiki.galaxyproject.org/Learn/Share

Thanks for your patience during this transition!

Jen
Galaxy team

On 10/2/13 6:46 PM, Theresa Stueve wrote:

Greetings,
   I have had two RNAseq files in queue to map with Top hat  in Galaxy 
Main since last Thursday (History began  Sept 19). I got word that NGS 
was stalled, my jobs were mistakenly believed to be moving afterwards 
when they weren't-
 but are now under review again. It has been a week now and the 2 
mapping jobs are still waiting to run.
   Can you tell me whether I should delete the jobs and re-run them as 
new? Is there a problem with my trimmed dataset? My concern is that 
these jobs are still "believed to be moving"  as was indicated by one 
of your galaxy stewards, but are actually still stalled in space.


One week is a long tme to wait for local jobs, no?
thank you very much for your help
https://main.g2.bx.psu.edu/u/trstueve/h/rnaseqjegcsc3wkrun130924-1


Theresa Ryan Stueve
510-225-8894  (text better than voicemail for quick 
response)


--
Theresa Ryan Stueve
510-225-8894 (text better than voicemail for quick response)



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Adding a tool to Galaxy Main Server

[Jennifer Jackson]

Hello,

New tools go into the Tool Shed, links with instructions are here:

http://usegalaxy.org/toolshed
http://wiki.galaxyproject.org/Tool%20Shed

We tweet new tool additions to let the community know about them, info 
and recent tweets are here:

http://wiki.galaxyproject.org/Galaxy%20on%20Twitter

If you are working with someone about incorporating a tool onto the 
public Main server, contacting them direct is generally the best path. 
Alternatively, after the tool is in the Tool Shed, you can write to us 
at outre...@galaxyproject.org to ask about adding it. No promises! Many 
tools in the Tool Shed are specifically intended for use in 
local/cloud/slipstream Galaxy instances.


Next time, sending to just one list is best, these all reach the same 
Galaxy core team. Galaxy-dev is best for reaching our community that 
focuses on tool development.

http://wiki.galaxyproject.org/Support#Mailing_Lists

Best,

Jen
Galaxy team

On 10/7/13 9:36 AM, Hamid Reza Hassanzadeh wrote:


Hi everybody,
We are going to add our gene prediction tool to Galaxy Main server, 
anybody know whom we should contact?

Thanks
--
Hamid Reza Hassanzadeh,
PhD Student & Graduate Research Assistant,
Bioinformatics Lab,
Center for Bioinformatics and Computational Genomics
Joint Georgia Tech and Emory Wallace H Coulter Department of 
Biomedical Engineering,

Department of Computer Science at Georgia Institute of Technology

office: KACB 1343


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] URL problem

[Jennifer Jackson]

Alper,

Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu 
mailing list?


I am posting it there in case it is still open. Please reply to let us 
know your current status.


Please drop galaxy-u...@bx.psu.edu from the to/cc on reply and future 
posts to this thread.


Thanks and sorry if this one got missed,

Jen
Galaxy team


On 8/26/13 10:43 AM, Kucukural, Alper wrote:

Hi,
I have a problem in galaxy to get host/domain name in two different 
pages.
First one is in the tool installation from toolshed, I got the error 
below,


#


  Not Found

The requested URL /admin_toolshed/prepare_for_install was not found on 
this server.


#

The second one is in the saved histories. When I click the buttons of 
the saved histories. I got the similar error like below.

#


  Not Found

The requested URL /history/list was not found on this server.

#

I haven't seen these any other pages yet.

My installation is working on LDAP authentication with Proxy. So, I 
could not find a place to set the domain or host name in these two 
places that they can actually find the requested URLs.


In the  paster.log file. I don't get any error when I install a tool 
or go to another history. It doesn't report any error.


Thanks for your help,

Alper Kucukural


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] RNAseq Map with Top Hat job in queue 4 days, 'waiting to run"

[Jennifer Jackson]

Hello Theresa,

Local jobs should run fairly quickly. But the NGS queue was stalled, 
then believed to be moving earlier (incorrectly by me), but now under 
review again. The grey queued jobs will eventually execute, so I 
wouldn't delete them quite yet.

http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

For high-priority work, a move to an alternate Galaxy solution is 
certainly an option, even more so given your deadline. A cloud Galaxy is 
one good choice - this is a sure thing but has associated costs. Other 
public servers are also potential choices - each has different tools 
available and other requirements - so check out these and see what may 
work. Links for you to review are here:

http://wiki.galaxyproject.org/BigPicture/Choices
http://wiki.galaxyproject.org/Cloud
http://wiki.galaxyproject.org/PublicGalaxyServers

Good luck, and thanks for the patience during our upgrade,

Jen
Galaxy team

On 9/30/13 7:56 PM, Theresa Stueve wrote:

Greetings,
   I would like to map some RNAseq data in Top hat in Galaxy Main- I 
only have 2 files but both have have been in queue 'waiting to run' 
since last Thursday (9/26)? I have a data meeting this Thursday and am 
gonna get trounced


can you advise? history is below

is there another galaxy I can try perhaps? I do appreciate that you 
all are expanding the universe

--
Theresa Ryan Stueve
510-225-8894  (text better than voicemail for quick 
response)




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] bwa indexing not automatic?

[Jennifer Jackson]

Hi Joshua,

Just to double check, you are running the latest stable distribution?

There are a few different BWA wrappers in the tool shed, maybe you are 
using a different one than previously? Using a custom reference genome 
from the history with bwa is possible with the wrapper with the owner 
"devteam" (assuming Galaxy is installed where there are suitable 
resources - same as command line bwa).


If you want to try again and report back any ongoing issues, please use 
the galaxy-...@bx.psu.edu mailing list to reach the development 
community (drop galaxy-u...@bx.psu.edu from the to or cc).


Thanks,
Jen
Galaxy team


On 9/27/13 7:37 PM, Joshua Orvis wrote:
I installed a new copy of galaxy today and then added the bwa_wrappers 
tool.  After I upload my reference genome and left/right reads I get 
output like this each time I try to run bwa for illumina:


The alignment failed.
Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwt_restore_bwt] fail to open file 
'/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'.
 Abort!
/bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I 
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat 
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat 
> /tmp/tmpMuj4l2/tmpUIdxXT
If I manually do the 'bwa index' command on dataset_4.dat it works but in the 
past this seemed to happen automatically.  Any clue what's going on here?


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] cleanup_datasets.py with postgresql 8.1

[Jennifer Jackson]

Posting to galaxy-...@bx.psu.edu to give the question better exposure to 
the development community.
Please _remove the galaxy-u...@bx.psu.edu mailing list from all replies_ 
- we want to avoid double posts.



For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev


On 9/26/13 7:29 AM, Malcolm Tobias wrote:


All,

My understanding is that the cleanup_datasets.py under 
scripts/cleanup_datasets should be compatible with 'older' versions of 
postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the 
scripts, it fails to clean any data sets. From the logs, I'm noticing 
messages like:


database_connection contains an unknown SQLAlchemy database dialect: 
postgresql


In my universe_wsgi.ini I've defined the database_connection as:

database_connection = postgresql://galaxy:@localhost:5432/galaxydb

and am confident it's working as Galaxy works fine, other than this 
problem with deleting older datasets.


The pgcleanup.py script isn't an option, as it requires postgresql 
>=9.1. I noticed yet another version of cleanup_datasets.py under cron 
which looks like it might be compatible with postgres, but am leary of 
trying it as I'm not sure what it means by "1: database directory to 
clean". I'm not sure what directory to point this to, nor am I 
confident that just deleting data from the directory is the safest thing.


Any suggestions on how to proceed?

Thanks!

Malcolm

--

Malcolm Tobias

314.362.1594



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] datacache & bowtie2 for mm9 ?

[Jennifer Jackson]

Hello Curtis,

The datacache was originally pointed to the data staging area and is now 
pointed to the data published area. The difference is that the published 
area contains data and location (.loc) files that are in synch and have 
completed final testing. It is your choice about whether to use the 
staged-only data - it depends how risk tolerant your project is and if 
you plan on testing. But, that said, I think it is almost certainly fine 
or our team wouldn't have staged it yet. A vanishingly small number of 
datasets are pulled back once they make it to staging, and this is why 
we were comfortable pointing datacache there in the first place (were 
unable to point to the published area at first, but wanted to make the 
data available ASAP).


Going forward - I can let you know that these indexes are very easy to 
create: one command-line execution, then add one line to the associated 
.loc file. Instructions are here, see "Bowtie and Tophat":

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

For one or few genomes, not a problem. For hundreds of genomes with 
variants, can become tedious even with helper tools and in our case, the 
processing interacted with disk that was undergoing changes (as we have 
been working on system configuration most of the summer). Also, with the 
Data Manager is now available, creating batch indexes for use via rsync 
become lower priority. Even so, I would expect more indexes to be fully 
published once the final configuration is in place, as many are already 
staged or close being staged (watch the yellow banner on Main).


Hopefully this helps to explain the data, guides you to making an 
informed decision, and aids with creating your own indexes as needed,


Thanks!
Jen
Galaxy team

On 9/18/13 1:04 PM, Curtis Hendrickson (Campus) wrote:


Folks,

First, I wanted to thank you for making the datacache available 
(http://wiki.galaxyproject.org/Admin/Data%20Integration; 
rsync://datacache.g2.bx.psu.edu). It's a great resource.


However, what is the best way to stay abreast of changes to what's in 
datacache, and understand how these indexes are computed?


We are currently upgrading to bowtie2, but I notice that the bowtie2 
indices for mm9, which used to be in


rsync://datacache.g2.bx.psu.edu/indexes/mm9/mm9*/bowtie2_index

have been removed, and only the hg19 genome has bowtie2 indices. Why 
only that one, and not the others?


Where are the scripts you use to make these indices, in case I want to 
create bowtie2 indices for other


So, how do I find out **why** they were removed? (Can I safely use the 
copy I have, or was there a problem with them?)


More generally, how do I understand the policies and logic behind the 
datacache indices, and be notified of changes, short of running my own 
periodic rsync/diff?


Finally, since I'm doing "reproducible research" is anything planned 
for systematically versioning genome indices, so I can easily tell 
what version of a system (ie, what BWA version) was used to create the 
index, and be sure that an index will not suddenly disappear.



Thanks,

Curtis

Research Associate/CTSA-Informatics Team

University of Alabama at Birmingham



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] which galaxy to use?

[Jennifer Jackson]

Hi Peter,

This is the correct list to post to (not owner, that is just for list 
subscription questions).

http://wiki.galaxyproject.org/MailingLists

Galaxy-dist is the stable release repository. Galaxy-central is the 
active development repository. Depending on how risk-tolerant your 
project is, either is a choice. You can also start with a dist base and 
pull from central individual changesets as desired, if you want to 
manage it that way.


I'll let the developers comment about nglims. You may need to post that 
as a brand new question (new thread) with that in the subject line to 
get the best replies. Or you can start by searching with the keyword 
here (or 'sample tracking' and narrow down what you need to know:

http://galaxyproject.org/search/getgalaxy/

These wiki's haven't been updated in a while, so I am not pointing you 
there first, but here they are for reference:

http://wiki.galaxyproject.org/Admin/Sample%20Tracking/

Best,

Jen
Galaxy team

On 9/17/13 11:10 AM, Peter Huang wrote:


Hi Galaxy,

I am trying to setup the production galaxy service at our place with 
Rocks Cluster and NGLIMS. I am confused as which one to use: 
galaxy-dist or galaxy-central.


My question is could I use galaxy-dist with nglims? I try to find how 
to do it, but couldn't.


Any suggestions?

Best,

Peter



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

[Jennifer Jackson]

Hi Carlos,

Nice this is being worked on.

Just wanted to mention a quick tip for loading barcode splitter output: 
1- right click on the output name & copy the link
2- open 'Get Data -> Upload File' tool, and paste link into box. Execute.
3- Repeat for all.

Data will load as dataset, no downloading/uploading required. I find that 
pasting all the links into a temp text file, then copy/paste all at once into 
the Upload tool speeds this up - as it then loads all in one go.

Not perfect, but maybe helpful for now.

Best,
Jen
Galaxy team

On Sep 10, 2013, at 11:49 AM, Carlos Borroto  wrote:

> Cool, I got a tweet about this tool from @GalaxyProject[1].
> 
> To further explain what I'm trying to accomplish here, as I realized
> not everybody might know what using "Multiple Output Files" and
> specifically "Number of Output datasets cannot be determined until
> tool run"[2] entails.
> 
> The current Barcode Splitter available on Galaxy Main and based on
> FASTX-toolkit by Assaf Gordon, makes all output files accessible
> through HTML links. This is not very convenient, as if you want to
> use, and you probably do, these outputs in a downstream analysis
> inside Galaxy, your only solution right now is to download the linked
> files in the HTML output and manually re-import then into Galaxy. The
> tool I wrote includes the option of writing the output files(splitted
> FASTA or FASTQ files) with a naming convention that can be used with
> Galaxy's "Multiple Output Files" so all results files are
> automatically added to your history. I believe you still can't easily
> use this tool upstream in a workflow. As I far as I can tell tools
> without a known number of outputs can't be used upstream in workflows.
> I do think you can accomplish some automation using the API, although
> I haven't tested this yet.
> 
> [1]https://twitter.com/galaxyproject/status/377497531745595392
> [2]http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
> 
> Best,
> Carlos
> 
> On Fri, Sep 6, 2013 at 1:58 PM, Carlos Borroto  
> wrote:
>> Hi,
>> 
>> I was wondering if I could get someone to test this new barcode
>> splitter I wrote. The main reason for me to duplicate the already
>> great fastx-toolkit based splitter, is so I can use galaxy's multiple
>> output capabilities.
>> 
>> You can find this tool in the testtoolshed for now(after some more
>> testing I will moved to the main toolshed):
>> http://testtoolshed.g2.bx.psu.edu/view/cjav/split_by_barcode
>> 
>> Hopefully I got Galaxy's tool dependency system right(it works on my
>> box, not that this says much) and installing this tool should be quite
>> easy.
>> 
>> I have to say big thanks to Biopython and this[1] anonymous soul for
>> making it quite easy to write the actual code doing the heavy lifting.
>> 
>> [1]https://gist.github.com/dgrtwo/3725741
>> 
>> Cheers,
>> Carlos
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] NoClassDefFoundError in Picard Paired Read Mate Fixer

[Jennifer Jackson]

Hello,

The easiest way to ensure that dependencies are set up correctly is to 
install tool dependencies directly from the Tool Shed:

http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency

You will want to use:
http://toolshed.g2.bx.psu.edu/
"package_picard_1_56_0"

For local instance help, please post to the galaxy-...@bx.psu.edu 
mailing list, as that is the best way to reach the development 
community. I am going to double post this reply, to resolve the question 
on the original galaxy-user and to give it visibility on the galaxy-dev 
list, but going forward on this thread (if needed) please remove 
galaxy-user from future replies.


Best!

Jen
Galaxy team


On 8/31/13 11:19 AM, Nicolas Quizon wrote:

Dear Galaxy Gurus,

I am a student and still new to Galaxy. I am encountering an error 
when trying to run the Picard Paired Read Mate Fixer with default 
settings on Galaxy. The code only runs for a few seconds before 
failing and displaying the error message.


## exit code=1; stdout=
[Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation 
INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] 
OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T 
SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO 
QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=50 
CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on 
Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; 
Picard version: 1.91()
[Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation 
done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=378470400
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.NoClassDefFoundError: 
org/itadaki/bzip2/BZip2InputStream
at 
net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84)
at 
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at 
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at 
net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76)
Caused by: java.lang.ClassNotFoundException: 
org.itadaki.bzip2.BZip2InputStream

at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 4 more

 For input I am using data that I have successfully mapped with BWA 
for Illumina. I currently have Python version 2.7.3 and Java version 
1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS.


Any help is greatly appreciated!

Thanks!


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] version_command tag problem

[Jennifer Jackson]

Hi Wolfgang,
I am going to re-post your question over to the galaxy-dev mailing list, 
which is best for local instance questions. To all: please remove the 
galaxy-user list from any replies.

Thanks!
Jen
Galaxy team
On 9/5/13 1:33 AM, Wolfgang Maier wrote:

Hi everybody,
I'm trying to add the version_command tag to my tools' xml
files, but I run into a problem here. Currently I have:
aln.py
--version
in my xml.
When I run the tool Galaxy tells me that it executed this:
python3 /home/me/galaxy-dist/tools/modmapmin/aln.py
--version &>
/home/me/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1035
but when I check that temporary file it's empty (and so is
the tool version line at the end of the run).
This is puzzling because when I run that exact command line
from my terminal, it writes
0.8.2
to the file just as it should.
Any ideas what goes wrong here?
Thanks and best wishes,
Wolfgang
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] about Galaxy

[Jennifer Jackson]

Hello,

To use Velvet, a local, cloud, or slipstream Galaxy is needed. Then the 
tool can be installed from the Tool Shed and used. The screencasts 
"Introduction to Galaxy ToolShed 1/2/3" walk through the general process 
when using CloudMan Galaxy:

http://vimeo.com/user20484153

http://wiki.galaxyproject.org/Cloud
http://wiki.galaxyproject.org/BigPicture/Choices

If you need help with set up, or just have more questions about these 
options, the list is: "galaxy-...@bx.psu.edu"

http://wiki.galaxyproject.org/MailingLists

Best,
Jen
Galaxy team

On 9/4/13 5:31 AM, Jingjing Peng wrote:

Hi,
Nowadays I am using Galaxy to analyze my data. It is really very good. 
But there is sth I cannot work it out by this program. My sequences 
were sequenced by  Illumina Miseq 2*250bp,paired end method. I want to 
assembly this large transcriptom sequences. I didn't find velvet in 
this website:https://main.g2.bx.psu.edu/ .
So how can I find it and make this work. I am sorry to trouble you. 
Thanks a lot.


Best wishes,

Jingjing Peng



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] URL problem

[Jennifer Jackson]

Hi Alper,
There may be permissions problems if just for these two links, but I am 
not an expert on this. Moving post over to the galaxy-dev list, which 
will give it better exposure to the development team and community. 
You'll want to post here directly with any future local install 
questions. http://wiki.galaxyproject.org/Support#Mailing_Lists

Best,
Jen
Galaxy team


On 8/26/13 10:49 AM, Kucukural, Alper wrote:

Hi,
I have a problem in galaxy to get host/domain name in two different pages.
First one is in the tool installation from toolshed, I got the error below,

#
Not Found

The requested URL /admin_toolshed/prepare_for_install was not found on this 
server.

#

The second one is in the saved histories. When I click the buttons of the saved 
histories. I got the similar error like below.
#
Not Found

The requested URL /history/list was not found on this server.

#

I haven't seen these any other pages yet.

My installation is working on LDAP authentication with Proxy. So, I could not 
find a place to set the domain or host name in these two places that they can 
actually find the requested URLs.

In the  paster.log file. I don't get any error when I install a tool or go to 
another history. It doesn't report any error.

Thanks for your help,

Alper Kucukural
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] No zebrafish Zv9 build

[Jennifer Jackson]

  
  
Hi Tiffany,

This build is included in the public Main Galaxy instance at
https://main.g2.bx.psu.edu (usegalaxy.org) and in the most current
CloudMain AMI (by default).

This is the full name:



If you are working with a local instance, then the genome would need
to be added. The original source we used is from UCSC
(http://genome.ucsc.edu). You can set this up yourself, or use our
indexes and loc files (as a base, edit out what you don't need, or
add what extra you want). Help is here:
http://wiki.galaxyproject.org/Admin/Data%20Integration
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If you question has been misunderstood, please help to clarify and
we can offer more advice,

Best,

Jen
Galaxy team

On 8/28/13 1:42 PM, Smith, Tiffany L
  wrote:


  
  
  I cannot work with Zv9 data because
galaxy does not seem to support it. Can you please add
Zv9/danRer7 to the database/build list?

Tiffany Smith
  
  
  
  
  ___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
  

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] adding new genome to local galaxy instance

[Jennifer Jackson]

Hi Vipin,

On 8/28/13 1:34 PM, Vipin TS wrote:

Hello,

I am slightly confused with adding a new genome to my local Galaxy 
instance, I am using the recent default branch 10411:c42567f43aa7 
(following the documentation at 
http://wiki.galaxyproject.org/Admin/Data%20Integration)


I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new 
Arabidopsis genome and updated 
~/galaxy-dist/tool-data/shared/ucsc/builds.txt, when I restarted my 
local instance, I am not finding the newly added genome in database.
Is it not showing up under the list of databases/genomes when you at 
these locations:


 1 - Get Data -> Upload File -> Genome: (pull down menu)
or
 2 - Click on the pencil icon for any dataset, first page of 'Edit 
Attributes' forms "Attributes -> Database/Build"


You mentioned restarting, which is good, because that is necessary. The 
next thing to double check is that the names are "exact" and that the 
files are tab delimited, not space delimited, and have no trailing or 
extra whitespace (this is easy to slip in by accident).


Or do you mean that it is not showing up as a target database/genome for 
a particular tool? Tools/groups of tools require additional set up, as 
explained on this page (also linked from the one you mention - which 
also has information about rsync of the indexes/loc files the public 
Main instance uses):

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If this doesn't help solve the issue, pls send more details, perhaps a 
sample of files, and we can help.


Jen
Galaxy team


any idea what is going wrong here ?

thanks,
--/Vipin



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini

[Jennifer Jackson]

 Original Message 
Subject: 	Re: how to add settings of TMPDIR=/scratch for sge/drmaa in 
universe_wsgi.ini

Date:   Tue, 13 Aug 2013 23:21:16 -0700
From:   tin h 
To: Jennifer Jackson 
CC: Galaxy Dev 




Thank you Jennifer.

I am not sure if my previous email got gabled up...
Just to be sure, I specified the following in universe_wsgi.ini
 default_cluster_job_runner = drmaa://-q default.q -V -v 
TMPDIR=/scratch/


when i start galaxy, looking at the console log, this is what I see:

galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 Loaded 
job runner 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa'
galaxy.jobs.runners.drmaa DEBUG 2013-08-14 14:08:14,885 Converted URL 
'drmaa://-q default.q -V -v TMPDIR=/scratch/' to destination 
runner=drmaa, params={'nativeSpecification': '-q default.q -V -v TMPDIR='}
galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 Legacy 
destination with id 'drmaa://-q default.q -V -v TMPDIR=/scratch/', url 
'drmaa://-q default.q -V -v TMPDIR=/scratch/' converted, got params:
galaxy.jobs <http://galaxy.jobs> DEBUG 2013-08-14 14:08:14,885 
nativeSpecification: -q default.q -V -v TMPDIR=



The parser has stopped at the / before scratch and ignored the rest :(


I did  refer to 
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster and tried 
to define job_conf.xml as





load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>




-q default.q -V -v 
TMPDIR=/scratch






But then galaxy won't start, giving me the error of:

Traceback (most recent call last):
  File 
"/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", 
line 37, in app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 95, in 
__init__

self.job_config = jobs.JobConfiguration(self)
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 
107, in __init__

self.__parse_job_conf_xml(tree)
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 
157, in __parse_job_conf_xml
self.default_handler_id = self.__get_default(handlers, 
self.handlers.keys())
  File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 
286, in __get_default

rval = parent.get('default')
AttributeError: 'NoneType' object has no attribute 'get'

I am not sure what the "default" refers to, doesn't seems to be the 
destinations default specified as I tried changing that name but the 
error message remains the same.


Any help so that I can pass TMPDIR=/scratch into SGE qsub would be 
greatly appreciated.



-Tin




--

I am riding to fundraise for the Cystic Fibrosis Foundation.  Please 
consider a tax deductible donation at 
http://www.cff.org/LWC/dsp_DonationPage.cfm?idEvent=23815&idUser=615989



~~~__oEngineering is the art of making 
compromises.
 ~~~ _ <_ Science is the reverse 
engineering of the compromises made by nature.
   ~~~  (_)/(_)Medicine is the hacking of the 
scientific knowledge base.   - A comp sci student :-)


On 8/13/13 7:28 PM, Jennifer Jackson wrote:

Hi Tin,

I am going to move this over to the galaxy-...@bx.psu.edu mailing list 
(good for local install questions) to give it better viability.


I am by no means the best person to help with this, so hopefully 
others will jump in, but just from looking at this I am wondering if 
you shouldn't be instead looking at the " 
job_conf.xml.sample_advanced" file. There is the default version as 
well, but it is probably not what you are looking for if you want to 
add custom logging scripts.


For universe_wsgi.ini, it seems like maybe the problem with the syntax 
is most likely the unknown "default_cluster_job_runner" variable and 
the double "=" in the line. Slashes should be fine unescaped here. But 
as I said, I think the other file is the place for the changes anyway, 
or maybe both, but using known variables and a single "=" per path.


But let's see what the developers think!

Jen
Galaxy team

On 8/12/13 3:49 PM, tin h wrote:


Hello galaxy gurus,Â

I am trying to configure a local galaxy server to submit to SGE using 
DRMAA,Â
it works, but I would like to specify the equivalent of "-v 
TMPDIR=/scratch" for qsub.


I tried updating universe_wsgi.ini with something like:
  default_cluster_job_runner =  drmaa://-q default.q -V -v 
TMPDIR=/scratch/
but that doesn't work because "/" is a delimiter, and I have not been 
able to find way to

[galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini

[Jennifer Jackson]

Hi Tin,

I am going to move this over to the galaxy-...@bx.psu.edu mailing list 
(good for local install questions) to give it better viability.


I am by no means the best person to help with this, so hopefully others 
will jump in, but just from looking at this I am wondering if you 
shouldn't be instead looking at the " job_conf.xml.sample_advanced" 
file. There is the default version as well, but it is probably not what 
you are looking for if you want to add custom logging scripts.


For universe_wsgi.ini, it seems like maybe the problem with the syntax 
is most likely the unknown "default_cluster_job_runner" variable and the 
double "=" in the line. Slashes should be fine unescaped here. But as I 
said, I think the other file is the place for the changes anyway, or 
maybe both, but using known variables and a single "=" per path.


But let's see what the developers think!

Jen
Galaxy team

On 8/12/13 3:49 PM, tin h wrote:


Hello galaxy gurus,Â

I am trying to configure a local galaxy server to submit to SGE using 
DRMAA,Â
it works, but I would like to specify the equivalent of "-v 
TMPDIR=/scratch" for qsub.


I tried updating universe_wsgi.ini with something like:
  default_cluster_job_runner =  drmaa://-q default.q -V -v 
TMPDIR=/scratch/
but that doesn't work because "/" is a delimiter, and I have not been 
able to find way to escape it. Â Is there any tricks for this?



Much thanks in advance for your help in this matter.
-Tin


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] adding reference genome

[Jennifer Jackson]

Hi Vijay,

For right now, using a Custom reference genome with these tools is the 
best solution:

http://wiki.galaxyproject.org/Support#Custom_reference_genome

This genome in Galaxy is sourced from UCSC, as you probably know:
http://wiki.galaxyproject.org/Support#Reference_genomes

The longer-term strategy for new/updated indexes will be worked out 
soon. Our immediate goal was to get the tools out on Main as soon as 
possible.


Thanks,

Jen
Galaxy team

On 8/13/13 1:20 PM, Vijay Kumar wrote:

Dear sir,
please add reference genome of Zebra finch genome in Bowtie2 and 
Tophat2 option in galaxy. thank u



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Galaxy Distribution Aug 12, 2013

[Jennifer Jackson]

*Galaxy Distribution **Aug 12, 2013*
/
/
/http://bit.ly/galaxy20130812/


*Highlights:*

 *

   Upgrades to *Data Manager* including improved installation actions

 *

   *Visualization* Framework tunings, plus updates to *Phyloviz*,
   *Scatterplot*, and *Trackster ***

 *

   *Workflows* include new reproducibility controls and editing features

 *

   Multiple *Tool Shed* enhancements, features, and tunings

 *

   Plus additional updates to the *UI*, *Admin* and *Core*, and *API*,
   an important *Security Fix*
   reminder, and *Bug Fixes*

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade: $ hg pull
 $ hg update release_2013.08.12

/Thanks for using Galaxy,/

The Galaxy Team


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] BWA missing index on reference genome

[Jennifer Jackson]

Hi Moritz,

Pls see below

On Jul 26, 2013, at 6:37 AM, Moritz Juchler  
wrote:

> Hey,
> 
> 1 I installed Galaxy locally.
> 2 I also have BWA installed and then used the 
> 3 shed repository to get the bwa wrapper.
> 4 I have the reference genome:
>> -rw-r--r-- 1 trr users  10509 2013-07-25 11:31 human_g1k_v37.dict
>> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta
>> -rw-r--r-- 1 trr users   6597 2013-07-25 19:41 human_g1k_v37.fasta.amb
>> -rw-r--r-- 1 trr users   6844 2013-07-25 19:41 human_g1k_v37.fasta.ann
>> -rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt
>> -rw-r--r-- 1 trr users   2746 2013-07-25 11:32 human_g1k_v37.fasta.fai
>> -rw-r--r-- 1 trr users  775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac
>> -rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa
>  
> 5 and I changed the bwa_index and bw_index_color.loc to the path
> /genedata/human_genome_GRCh37/hg19.fa

This is the problem - the path must point to the full name of the fasta file. 
In your case "human_g1kv_v37.fasta".

Using the name without the fasta as the base name in other fields as the unique 
"dbkey" is a good practice.

Hopefully this helps,

Jen
Galaxy team


> 
> 6 This is my $PATH
>> trr@portalmoritz:~> echo $PATH
>> /home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19
> 
> Is there anything I am missing? I would be glad about some help.
> Best
> Moritz
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

Jennifer Hillman-Jackson
Galaxy Support & Training
http://galaxyproject.org___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Galaxy Server Questions

[Jennifer Jackson]

Hi Zain,

The minimum requirements for Galaxy are pretty much any recent model 
computer. A basic install will load and run within a very short amount 
of time, following the instructions at:

http://getgalaxy.org

Advanced tools come from the Tool Shed. These are installed separately. 
No programming is needed, but some very basic unix skills are required, 
as they would be for ongoing server maintenance. The Tool Shed is one of 
the best documented parts of Galaxy, so you should be able to find all 
the answers here, or this is the right list to use for questions about 
local installs (galaxy-...@bx.psu.edu):

http://wiki.galaxyproject.org/Tool%20Shed

However, running a production instance that is intended to run compute 
intensive tools (such as Tophat2), and where you have some throughput 
goals, will require more substantial resources. This is always a 
difficult question to answer since so much depends on the tools used and 
the data volume. But in general, minimum requirements are about around 
the same as what those underlying tools would require on their own, if 
run line-command. So for Tophat or Tophat2, and really the entire Tuxedo 
RNA-seq tool package, you might be able to get by on 8G memory and 2 or 
4 cores. But, it will probably be slow and if you are running replicates 
through Cuffdiff at the end, you might run out of memory if the files 
are large and the genome is large (such as human). And if you are are 
hosting a web Galaxy at the same time with visualizations and such, 
well, this is why systems are often set up with clusters. With all of 
these will be competing for the same resources, going low can work, but 
this will be something that will have to be managed/tested, and it will 
change through time as tools upgrade.


You could test this out by setting up a cloud instance with the hardware 
you plan to use, loading some of your data, and running your workflow to 
see how this benchmarks. Have users on the instance while you are doing 
this - to judge performance. Cloud installations come with many of the 
advanced tools and data indexes already installed/configured, so this 
would be less investment than buying the hardware first and finding out 
later it was not not enough.

http://usegalaxy.org/cloud

And of course Slipstream Galaxy is an option. The whole intention here 
is to make a complete package with tools & data already configured, in a 
system that has enough compute capability to do the work, for 
scientists/labs who do not want to deal with administrative tasks or 
work in the cloud (for whatever reason).

http://bioteam.net/slipstream/galaxy-edition/

Good luck with your decision! Other are welcomed to comment about how 
they have set up their system.


Jen
Galaxy team

On 7/15/13 7:14 AM, Zain A Alvi wrote:

Hi Jen,

I hope this reaches you well. I have a small question in regards to 
setting up a galaxy server. My mentors and I are looking into buying a 
server for doing NGS analysis through the use of Galaxy. We saw that 
slipstream's specifications for hardware to be the following:


CPU: 2x Intel Xeon Processor E5-2690, 8 core (16 cores total)
RAM Memory: 12x 32GB RDIMM (384 GB) with option to upgrade it to 512 GB
Storage (Hard Drive space): 7x 3TB SAS 6 Gbps (16 TB usable) with 1 x 
100GB Solid State Disk

Power: Dual Pedundant Power Supplies
Network: Dual Gigabit Network Adapter

We are wondering what can be the minimum server hardware 
specifications that Galaxy be run on.


Our second question is if we install Galaxy on the server, do all the 
tools currently available on Galaxy come pre-installed on it or do we 
have to program (Via Perl and Python) and install each of those tool 
sets ourselves.  If we have to install those tools ourselves, is there 
a guide that we can do so? Lastly, how can we upgrade the tool sets 
such as Tophat 1.44 to Tophat 2 on this server. I was wondering about 
the last question as Tophat 1.44 is available on the main Galaxy 
server whereas Tophat 2 is available on the test Galaxy server.


Sorry for so many questions. Thank you again for all the great help.

Sincerely,

Zain


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] BAM pileups bugging out

[Jennifer Jackson]

Hi Andrew,

If you want to run the tool "Filter pileup on coverage and SNPs" on 
dataset #21, change the datatype to be "pileup". Then it will show up 
under the list of inputs. Be sure to set the forms options for a 
10-column pileup input when you run it.


Change the datatype by clicking on the pencil icon for the dataset, to 
open the Edit Attributes form in the center panel. Click on the 
"Datatype" tab, then enter pileup, select it from the list, and save. 
Allow the metadata to finish detecting on it's own.


Hopefully this helps,

Jen
Galaxy team

On 6/24/13 5:11 PM, Andrew Guo wrote:
This is on the public instance. I can share my history with you right 
here...


https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101


On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote:


Hi Andrew,

Is this on a local instance or the public Main Galaxy instance at
usegalaxy.org <http://usegalaxy.org> (https://main.g2.bx.psu.edu)?

Also, the exact tools being used and the order is not clear. Maybe
a step is missing from what is listed? (I am just guessing) If you
are using the public Main instance, you can share a history with
me and I can provide feedback. If this is on your instance, could
you list the tools by name, in the order used, with key parameters
(e.g. "Generate pileup from BAM dataset" with option 10-column
pileup)?

It sounds like there might be a mix-up about the file formats
being used as inputs to tools. It may be something that can be
resolved by reassigning the datatype or by adjusting the tool(s) used.

Best,

Jen
Galaxy team


On 6/24/13 1:10 PM, Andrew Guo wrote:

After using tools to convert a SAM to a BAM file, I am trying to
filter the BAM pileup. However, the filter BAM tool is not
picking up on the dataset that I just created. It should show up
under 10 column pileup, but an error message is saying "History
does not include a dataset of the required format/build". Could
you provide any insight into this?

Thanks,
Andrew


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


-- 
Jennifer Hillman-Jackson

Galaxy Support and Training
http://galaxyproject.org




--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] BAM pileups bugging out

[Jennifer Jackson]

Hi Andrew,

Is this on a local instance or the public Main Galaxy instance at 
usegalaxy.org (https://main.g2.bx.psu.edu)?


Also, the exact tools being used and the order is not clear. Maybe a 
step is missing from what is listed? (I am just guessing) If you are 
using the public Main instance, you can share a history with me and I 
can provide feedback. If this is on your instance, could you list the 
tools by name, in the order used, with key parameters (e.g. "Generate 
pileup from BAM dataset" with option 10-column pileup)?


It sounds like there might be a mix-up about the file formats being used 
as inputs to tools. It may be something that can be resolved by 
reassigning the datatype or by adjusting the tool(s) used.


Best,

Jen
Galaxy team

On 6/24/13 1:10 PM, Andrew Guo wrote:
After using tools to convert a SAM to a BAM file, I am trying to 
filter the BAM pileup. However, the filter BAM tool is not picking up 
on the dataset that I just created. It should show up under 10 column 
pileup, but an error message is saying "History does not include a 
dataset of the required format/build". Could you provide any insight 
into this?


Thanks,
Andrew


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

[Jennifer Jackson]

Hi Elwood,

It sounds like you are getting closer, and that the instructions a few 
days ago from Jeremy are helping:

http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none

For each of these tools in #2, you will need to install them according 
to the instructions that comes with them from the source. However, there 
is one change I can mention. Symbolic links pointing from 
bowtie->bowtie2 and tophat->tophat2 are likely to be present in the 
default installation. You will want to remove those. Galaxy makes a 
clear distinction between the versions of the tools.


So, you have added tool's as required following the instructions in this 
wiki:

http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

And, in #3, you say that you have started to follow the instructions in 
this wiki:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Jeremy also sent you the links about how to obtain and set up the 
genomes and indexes.


Some of this does require limited unix-command line actions and file 
editing. The instructions are detailed, and some have command lines, 
because not all, as the exact thing to type can vary. If the 
line-command is entirely new, I wonder if there is someone locally with 
unix experience at your site that you can get help from? This last part 
should not take very long.


Best,
Jen
Galaxy team

On 6/20/13 8:45 AM, Elwood Linney wrote:


I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink 
suite to the mac

3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to 
introduce my large datasets on the some computer into Galaxy through 
Admin changing some permissions


but my minimal knowledge of unix commands and tricks has me stymied

Question:
If my primary purpose is to use this local instance for the analysis 
of RNAseq data within my lab, what is the simplest way of connecting 
the programs to the Galaxy framework?


While from reviewing info on the Galaxy website I am only guessing 
that adding them to $PATH might be the easiest way for me to do this 
(but I am not exactly sure what this means or specifically how I would 
do it in my case).  However, I do initiate the running of Galaxy by sh 
run.sh on my terminal and visualizing things via my localhost port.  
There is some indication from the wiki I found that this might not be 
good for a system initiated by sh run.sh.


[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under 
"Local Jobs"


I would appreciate any specific advice on this.

Sincerely,

Elwood Linney
DUMC


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] [galaxy-user] How do I add Ray to Galaxy Central in the tool shed ?

[Jennifer Jackson]

Hi again,

On Jun 13, 2013, at 1:23 PM, Sébastien Boisvert 
 wrote:

> Hi,
> 
> On 12/06/13 05:50 PM, Jennifer Jackson wrote:
>> Hi Sébastien,
>> 
>> This all looks fine, except for the part about including this in the
>> distribution. As James stated, we are moving to a model where eventually
>> all tools will be sourced from the Tool Shed. That is where you should
>> create your repository.
> 
> So if someone installs galaxy-dist, the person will have to pick up each tool 
> in the tool shed. Is that correct ?

Not all right now, just the ones not in the distribution that they want to use. 
These are mostly wrappers - 3rd party binaries are always distinct installs, 
sometimes automatic, as the wiki explains.

> 
> Will the schema of XML files remain the same ?

The tool XML is unchanged. But, the section for the tool is included in the 
master tool config XML, upon install, if I am interpreting this correctly. 
Again, the Tool Shed wiki is one of the best documented parts of Galaxy and has 
the details per use-case. You'll want to follow those instructions and follow 
the News Briefs for updates.

> 
>> Whether or not to have the repo binaries
>> self-install & config or not will be up to you.
> 
> You mean that some apps will self-install and other will require the 
> intervention of a system administrator.

Yes.

> 
>> 
>> Going forward, you probably will want to start up a new thread for new
>> questions and have discussions on the galaxy-...@bx.psu.edu mailing
>> list. This will give your questions the most exposure to the development
>> community.
>> http://wiki.galaxyproject.org/MailingLists#The_lists
> 
> You are right, I should have posted to -dev in the first place. Sorry.
> 

No problem! We are here to help. You'll  just find the development community 
even more helpful with local install and tool development feedback as you get 
more involved. That list gives your questions the best exposure to them. The 
Galaxy project is created from the inputs of many people - the core team and 
our community.

Best wishes for your project,

Jen 

> 
> So my deliverable to add Ray in galaxy is 2 XML files. Thanks.
> 
>> Take care,
>> 
>> Jen
>> Galaxy team
>> 
>> On 6/12/13 8:05 AM, Sébastien Boisvert wrote:
>>> On 06/06/13 02:32 PM, James Taylor wrote:
>>>>> I want to add Ray (a scalable de novo assembler for genomes and
>>>>> metagenomes)
>>>>> to Galaxy.
>>>> 
>>>> And I really want you to do this!
>>>> 
>>>>> I will also have to write a wrapper for Ray to prepare the command
>>>>> line from
>>>>> the options provided by the
>>>>> Galaxy API.
>>>>> 
>>>>> 
>>>>> But where is stored the executable (in my case, where is sdtored Ray) ?
>>>>> 
>>>>> Does Galaxy include the specs to build all the tools available in
>>>>> Galaxy-Central ?
>>>> 
>>>> No, we are gradually moving all the tools out of galaxy-central into
>>>> the Tool Shed. You probably want to look at this page:
>>>> 
>>>> http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
>>> 
>>> 
>>> From what I understand, I need to write 2 XML files in order to allow
>>> people to add Ray to their Galaxy instances:
>>> 
>>> * ray.xml
>>> * tool_dependencies.xml
>>> 
>>> These two files are self-contained -- that is Galaxy will install
>>> everything using tool_dependencies.xml (in my case,
>>> Open-MPI and Ray will be installed from source using the GNU compiler).
>>> 
>>> 
>>> Can I put these files directly in
>>> 
>>>galaxy-dist/tools/sr_assembly/ray/
>>> 
>>> ?
>>> 
>>> I suppose these 2 XML files will be distributed in galaxy-dist, but
>>> like Velvet, Ray won't be enabled by default in tool_conf.xml
>>> as assembly is more costly than mapping.
>>> 
>>> 
>>> Then, I need to add this to galaxy-dist/tool_conf.xml:
>>> 
>>> 
>>>   
>>>   
>>> 
>>> 
>>> 
>>> And finally, I just need to restart Galaxy.
>>> 
>>> 
>>> Is that correct ?
>>> 
>>>> 
>>>> Which describes how you can add a recipe to the toolshed that will
>>>> install the Ray binaries.
>>> 
>>> ___

--
Jennifer Hillman-Jackson
Galaxy Support & Training
http://galaxyproject.org
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] disk space usage

[Jennifer Jackson]

Hello Katie,

When you deleted the datasets, did you also delete them permanently 
(purge them)? If you view the history (and all histories) under history 
menu's option "Saved Histories", the total size will be noted, which can 
give you an idea about where the data in your account is located.


Use the history menu's option "Include Deleted Datasets" to view your 
deleted datasets, to see the status. From here you can permanently 
delete them individually by using the links in each. Or, you can 
permanently delete all deleted datasets in one step by using the option 
"Purge Deleted Datasets". Examining hidden datasets is also recommended 
if you still have data that is not accounted for.


More about Delete vs Permanently Delete is in our wiki here:
http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently

Remember that it can take some time for the database to update the usage 
statistics in the web interface after permanently deleting data. This 
should be less than an hour, and usually much quicker.


Looking for data this way solves almost all disk usage issues, but 
please let us know if you need more help,


Jen
Galaxy team

On 6/7/13 5:20 PM, Katie Kathrein wrote:

Hi,

I am having an issue with disk space.  I had some problems with 
loading datasets and ended up deleting a few that had errors.  Now 
things are fine, except that my disk space says 90% is being used, yet 
I only have about 70 GB of data right now.  Please help!


Thanks!
Katie


Katie Kathrein, Ph.D.
Zon Lab
Children's Hospital Boston
Karp Research Laboratories, 7005H
1 Blackfan Circle
Boston, MA 02115
kkathr...@enders.tch.harvard.edu 



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error in getting updates from server

[Jennifer Jackson]

Hello Mather,

Queued jobs should not be deleted and restarted, but allowed to execute. 
The server is very busy at this time and NGS mapping jobs are among 
those jobs that are in the busiest queue.

http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute

Just to let you know, sometimes it can appear that jobs are still 
waiting/executing when in fact they have completed. This happens when 
the history view becomes outdated. Clicking on the refresh icon (double 
arrow) at the top of the history panel will ensure that the most current 
dataset status is loaded in the history panel.


Hopefully this helps to clarify the job running process,

Jen
Galaxy team

On 6/7/13 1:44 PM, Mather Ali Khan wrote:

Hi,
Two days earlier i have executed my file for tophat, since then it is 
still in gey color and not getting any updates from server.

Should i delete the executed file and run again?
Please help me out.
Thanks
Mather

--
*Mather Ali Khan, Ph.D.*
*247, Bond Life Sciences Center*
*1201 Rollins Street*
*University of Missouri-Columbia*
*Columbia, MO, 65211, USA
*
Think Green - don't print this email unless really needed


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] June 3, 2013 Galaxy Distribution

[Jennifer Jackson]

June 3, 2013 Galaxy Distribution 




*Complete News Brief 
*


*Highlights:*

 *

   Visualization tool updates to Scatterplot
   
   and Trackster
   .

 *

   Job distribution, error tracking/management, and reporting function
   improvements to Admin
    &
   Core .

 *

   Multiple Tool
   
   updates, History and Dataset
   
   upgrades, and other related UI
   
   enhancements.

 *

   New features and fixes added to the Tool Shed
   
   and related components.

 *

   Python 2.5 Support /officially ended/
   
.


 *

   Plus newly merged Pull Requests
   
   and links to tickets covering key Bug Fixes
   .

/
http://getgalaxy.org/  

/http://bitbucket.org/galaxy/galaxy-dist/  


/http://galaxy-dist.readthedocs.org/

//

new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade: $ hg pull
 $ hg updaterelease_2013.06.03

/Thanks for using Galaxy,/

The Galaxy Team 

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Problem with ftp connexion to Galaxy

[Jennifer Jackson]

Hello,

New accounts (created this week) cannot FTP at this time. We hope to 
have this resolved soon. Please feel free to contact us for an update if 
this is still a problem by next Friday.


Our apologies for the inconvenience,

Jen
Galaxy team

On 5/22/13 6:34 AM, Fabrice BESNARD wrote:

Hello,

I am a new Galaxy User.
I am definitely not an expert in informatics, so my questions may sound
silly to you... I apologize if it is the case!
Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla,
and the error message suggests that it comes from an incorrect password to
Galaxy.

Here is the messages displayed by Filezilla (french version) while trying
to connnect:

Statut :Résolution de l'adresse de main.g2.bx.psu.edu
Statut :Connexion à 128.118.250.4:21...
Statut :Connexion établie, attente du message d'accueil...
Réponse :   220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP)
[:::128.118.250.4]
Commande :  USER fbesn...@biologie.ens.fr
Réponse :   331 Password required for fbesn...@biologie.ens.fr
Commande :  PASS ***
Réponse :   530 Login incorrect.
Erreur :Erreur critique
Erreur :Impossible d'établir une connexion au serveur

I was puzzled by this error message, because I do connect as user in the
Galaxy website. As recommended, I use the SAME login (=email
adress)/Password in both Galaxy login page and filezilla.
I tried to reset my password and connect again: I could connect directly
to the web site, but I still failed establishing a connexion via
filezilla.

I just created an account yesterday to Galaxy (Tuesday, 21th of May 2013).
Maybe I should just wait a little bit for a synchronization of the user
connexion parameters, should I?

Moreover, my Filezilla is working with other ftp server, so that I think
we can exclude that the problem comes from there.

I extensively looked for similar trouble reports on internet (googling
with other terms "530 Login incorrect"). Unfortunately, I could not solve
this problem. However, I found that you were asked one year ago for a
similar problem in this page:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010457.html But I
must confess that I could not understand most of what was written in this
informatic experts discussion! By the way, my system is not an ubuntu, so
I think that the solution you suggested would not work in my case.

Here are the characteristics and versions of the systems installed on my
computer:
Operating system: Windows 7 professionnal, 64bits
Filezilla Client 3.7.0.1
Firefox 20.0.1

I really thank you for reading this help message and I hope that you could
explain me how to solve my problem.

I look forward to reading your answer soon,
Best regards,



--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Problem about main.g2.bx.psu.edu is taking too long to respond.

[Jennifer Jackson]

Hi Chureerat,

We emailed about this yesterday, but for others who may have noticed a 
few interruptions, I wanted to reply on this.


There were some known, intermittent, peak usage times earlier in the 
week, but these should be mostly resolve. Galaxy is still busy, so if 
this does come up again, just wait a few minutes, then try the query again.


Take care,

Jen
Galaxy team

On 5/23/13 7:04 AM, จุรีรัตน์ โพธิ์แก้ว wrote:

Dear Galaxy team,

I have problem with my galaxy because I can 't check my data.
I refresh my page several time but it keep report the connection has 
timed out.


Please let me know what should I do to fix this problem.

Thanks,
Chureerat


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] populating the pull-down menu: reference genomes (built-in index)

[Jennifer Jackson]

Hello Jeannette,

Data is available from our rsync server, as explained here:
http://wiki.galaxyproject.org/Admin/Data%20Integration
See "Get the data"

If you need to make indexes that we do not have, each tool's original 
documentation will have general instructions and the Galaxy .loc file 
has instructions for how to configure so that these are usable by tools. 
We also give specific instructions for many here:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Hopefully this helps,

Jen
Galaxy team

On 5/22/13 10:45 AM, Staheli, Jeannette wrote:


Hi,

We are trying to put a few reference genomes into the built-in index 
for bwa, bowtie, bowtie2 and tophat.  For the human hg19 we can find 
those.  However, we also like to upload the Rhesus macaque genome and 
haven't been able to find an indexed version at NCBI or other places.


Are other genomes pre-indexed for these applications somewhere?

How do those files look like exactly (extensions, number of files 
needed, etc.)?


How would we index the Rhesus genome for the above mappers if they are 
not available in an indexed form?


Thank you,

Jeannette

CONFIDENTIALITY NOTICE: This e-mail message, including any 
attachments, is for the sole use of the intended recipient(s) and may 
contain confidential and privileged information protected by law. Any 
unauthorized review, use, disclosure or distribution is prohibited. If 
you are not the intended recipient, please contact the sender by reply 
e-mail and destroy all copies of the original message.



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/