Re: [galaxy-dev] good practice for Galaxy admin and updates ?

[Hans-Rudolf Hotz]

Hi Julie

We do something similar, I have described it here:

https://galaxyproject.org/admin/ten-simple-steps-galaxy-as-a-service/#rule-10-keep-the-galaxy-software-and-yourself-up-to-date


Regards, Hans-Rudolf


On 09/03/2018 01:19 PM, julie dubois wrote:

Hi Galaxy Community,

I manage a Galaxy local instance on a standalone station since 6 years.
Regarding the numerous troubleshoots I have encountered (and the very
long time I spent) during these years with Galaxy updates trying to
minimize impact for my users, trying in the same time to keep safe
our customization of this instance. I'm wondering about the best solution
to manage my instance and to test my own dev and also Galaxy updates
before pushing them on
my production server.

So I want to test a new way and I'd appreciate community feedback on this idea
or let me know if other practices could be more appropriate in my situation.
So my basic idea is:

First install a new Galaxy from scratch, not by cloning the stable branch of
Galaxy but by forking it. And use the master branch of this fork as
production server.
Then to manage an update of the Galaxy stable, my idea is to make a
test branch on my
fork, then pull Galaxy update on this test branch and run this test instance as
a dev server in another station to be sure that update will not override our
customization or any crucial tools/functionality for my users.
Finally when I'll be sure this update is safe, I'll merge the test branch with
the master branch of my forked Galaxy.


Is anyone already acting in this way? Is it a good (the best) way to manage
local instance of Galaxy? Have you other good practices?

Thanks a lot for your help.

Julie
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Re: [galaxy-dev] Setting up Galaxy Reports

[Hans-Rudolf Hotz]

Hi Christopher

Well, the look of the reports pages are very basic to start with.

what happens when you start the reports with "reports.ini" (i.e.: the 
"old way", see: 
https://docs.galaxyproject.org/en/release_17.05/admin/reports.html


Hans-Rudolf


On 08/31/2018 03:51 PM, Previti wrote:

Dear Hans-Rudolf and list participants,

We would like to set up the galaxy reports tool on our version 17.09
instance and we succeeded partially after modifying the "reports.yml" to
point to our postgresql database.

The webpage is generated, with all the stats, but looks very basic and
the appropriate style-sheets are probably not found...

Any advise on how to set this up properly would be very welcome.

Best regards,

Christopher


On 08/17/2017 04:56 PM, Hans-Rudolf Hotz wrote:

Hi Evan

I assume you are talking about the 'reports' tool?

Have a look here:

https://galaxyproject.org/admin/usage-reports/
https://docs.galaxyproject.org/en/latest/admin/reports.html

Additional (system) information about each executed job can be logged
by activating plugins in the "./config/job_metrics_conf.xml" file.

https://galaxyproject.org/admin/config/job-metrics/


Hope this helps
Regards, Hans-Rudolf



On 08/17/2017 04:25 PM, evan clark wrote:

I remember there previously being an additional tool that ran on a
different port from galaxy that allowed for monitoring of performance
and jobs running. Is this tool still packaged with galaxy and if so how
can it be activated.
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[galaxy-dev] European Galaxy Days, 19/20 November 2018 in Freiburg, Germany.

[Hans-Rudolf Hotz]

Dear all


We are happy to announce the European Galaxy Days which will be held 19 
and 20 November 2018 in Freiburg, Germany.



https://galaxyproject.org/events/2018-europe-dev/



Similar to the events we organized in 2016, 2014 and 2012 the aim is to 
discuss the status of the Galaxy project, new developments, interfaces 
to other systems, extensions and best practice in reproducible research.


The program is planed as follows:

Monday, November 19th
We intend to have a full day of talks from you. We especially encourage 
Galaxy User to present their work with Galaxy.
Please indicate your interest in presenting when you register (we will 
then get in contact with you). Or contact us directly.


Tuesday, November 20th
This day is more on the technical side, with presentation, tutorials and 
hands on exercises. Currently we plan to discuss/present:

 - Galaxy and Machine learning
 - Single Cell RNA Seq analysis with Galaxy
 - Combining Galaxy with Shiny



Registration is now open (space is limited). There will be no conference 
fee. Though, you need to cover for your food and accommodation (we are 
currently looking for sponsors to cover the lunches on the two days). We 
recommend you register soon to secure your spot:



https://tinyurl.com/EGD2018


Looking forward to see many of you in Freiburg

Regards,
Jean-François, Bjoern and Hans-Rudolf


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Re: [galaxy-dev] Expose Command Line in Galaxy

[Hans-Rudolf Hotz]

Hi Matthias

If for whatever reasons the  "i" (view details) icon doesn't work for 
you, you can use the Galaxy Report Webapp (for docker installations see: 
https://github.com/bgruening/docker-galaxy-stable#Galaxy-Report-Webapp ) 
as an alternative.


You can find your (failed) job via "Jobs in error per day this month". 
Once you clicked on the 'job id' you will get the executed command line/



Hope this helps.
Regards, Hans-Rudolf





On 07/10/2018 08:58 AM, Matthias Enders wrote:

Dear Galaxy Community,

is there any possibility to expose the command line call, generated within 
galaxy?

We searched the net and found this discussions:
https://github.com/galaxyproject/galaxy/issues/3252
https://github.com/galaxyproject/galaxy/issues/2954

But both are on the exposure to non-admin users. Within our instance we see the 
command line call nor for admin, neither for normal users!

The problem, behind the question is the error message: "An invalid option was 
selected for database, 'myCoolDatabaseName', please verify." In Blast 
(toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01)

Local (directly from command line, without Galaxy in between) the blast works 
fine.

We are using the 18.05 Docker Galaxy Version.

Thanks in advance!

Mit freundlichen Grüßen

Matthias Enders
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-Ursprüngliche Nachricht-
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Today's Topics:

1. From Paste to uWSGI (Jochen Bick)
2. Re: From Paste to uWSGI (Peter Briggs)
3. Re: From Paste to uWSGI (Martin Čech)


--

Message: 1
Date: Mon, 9 Jul 2018 13:49:23 +0200
From: Jochen Bick 
To: "galaxy-dev@lists.galaxyproject.org"

Subject: [galaxy-dev] From Paste to uWSGI
Message-ID: <1a0f33ad-938c-64d5-8db8-28914a5ca...@usys.ethz.ch>
Content-Type: text/plain; charset="utf-8"; format=flowed

Hi all,

we would like to update to 18.05 and thereby also update our Paste Server.

https://docs.galaxyproject.org/en/latest/admin/scaling.html

Is there any tutorial on how to update from Paste to uWSGI?


Cheers Jochen

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*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
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Message: 2
Date: Mon, 9 Jul 2018 15:31:16 +
From: Peter Briggs 
To: Jochen Bick ,
"galaxy-dev@lists.galaxyproject.org"

Subject: Re: [galaxy-dev] From Paste to uWSGI
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hello Jochen

I'm not aware of a tutorial but here are some observations from my (very) 
recent experiences upgrading a local paste-based 17.09 instance to a 
uwsgi-based 18.05 configuration. It's not comprehensive because the 
configuration will depend on decisions you need to make based on your local 
setup, but it might be helpful as a starting point.

Before beginning:

-- Commit to migrating from galaxy.ini to galaxy.yml (if not done previously)

Even though its possible to stick with the old galaxy.ini file, it seems best 
to move to the new format - my feeling is, probably the migration will have to 
happen at some point anyway, and also the documentation is more focussed on the 
newer galaxy.yml v

Re: [galaxy-dev] MySQL errors and warnings with a fresh install of Galaxy 18-05

[Hans-Rudolf Hotz]

Hi Fred

Sorry, I don't have an answer I am just wondering: If you start from 
'scratch', why don't you use PostgreSQL?


Regards, Hans-Rudolf



On 06/13/2018 05:41 PM, SAPET, Frederic wrote:

Hi,

I try to install galaxy 18-05. My database backend is MysqL (5.7.11-4
Percona Server)

I start from scratch (drop database, new directory with galaxy files
fetched with git)

So the database is first created when run.sh is used : :

Creating database for URI [mysql://….

I see warnings about duplicated indexes and OperationalError from
SQLAlchemy.

Some tables are then missing in my database
(workflow_invocation_output_dataset_collection_association and
workflow_invocation_output_dataset_collection_association).

And fields are still present (ie in request table : library_id and
folder_id)

Could you please help me ?

Thank you.

Fred


grep  "^OperationalError:" FirstRun.log  | cut -f 2- -d ","


"Cannot drop index 'ix_request_library_id': needed in a foreign key
constraint") [SQL: u'\nALTER TABLE request DROP COLUMN library_id']
(Background on this error at: http://sqlalche.me/e/e3q8)

"Cannot drop index 'ix_request_folder_id': needed in a foreign key
constraint") [SQL: u'\nALTER TABLE request DROP COLUMN folder_id']
(Background on this error at: http://sqlalche.me/e/e3q8)

"BLOB/TEXT column 'annotation' used in key specification without a key
length") [SQL: u'CREATE INDEX ix_page_annotation_association_annotation
ON page_annotation_association (annotation)'] (Background on this error
at: http://sqlalche.me/e/e3q8)

"Cannot drop index 'sequencer_id': needed in a foreign key constraint")
[SQL: u'\nALTER TABLE request_type DROP COLUMN sequencer_id']
(Background on this error at: http://sqlalche.me/e/e3q8)

"BLOB/TEXT column 'guid' used in key specification without a key
length") [SQL: u'CREATE UNIQUE INDEX ix_tool_id_guid_map_guid ON
tool_id_guid_map (guid)'] (Background on this error at:
http://sqlalche.me/e/e3q8)

"BLOB/TEXT column 'layout' used in key specification without a key
length") [SQL: u'CREATE INDEX ix_form_definition_layout ON
form_definition (layout)'] (Background on this error at:
http://sqlalche.me/e/e3q8)

"BLOB/TEXT column 'notification' used in key specification without a key
length") [SQL: u'CREATE INDEX ix_request_notification ON request
(notification)'] (Background on this error at: http://sqlalche.me/e/e3q8)

"BLOB/TEXT column 'data_manager_id' used in key specification without a
key length") [SQL: u'CREATE INDEX
ix_data_manager_job_association_data_manager_id ON
data_manager_job_association (data_manager_id)'] (Background on this
error at: http://sqlalche.me/e/e3q8)

"Identifier name
'workflow_invocation_output_dataset_collection_association_ibfk_1' is
too long") [SQL: u'\nCREATE TABLE
workflow_invocation_output_dataset_collection_association (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_id INTEGER,
\n\tworkflow_step_id INTEGER, \n\tdataset_collection_id INTEGER,
\n\tworkflow_output_id INTEGER, \n\tPRIMARY KEY (id), \n\tFOREIGN
KEY(workflow_invocation_id) REFERENCES workflow_invocation (id),
\n\tFOREIGN KEY(workflow_step_id) REFERENCES workflow_step (id),
\n\tFOREIGN KEY(dataset_collection_id) REFERENCES
history_dataset_collection_association (id), \n\tFOREIGN
KEY(workflow_output_id) REFERENCES workflow_output (id)\n)\n\n']
(Background on this error at: http://sqlalche.me/e/e3q8)

"Identifier name
'workflow_invocation_step_output_dataset_collection_association_ibfk_1'
is too long") [SQL: u'\nCREATE TABLE
workflow_invocation_step_output_dataset_collection_association (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tworkflow_invocation_step_id
INTEGER, \n\tworkflow_step_id INTEGER, \n\tdataset_collection_id
INTEGER, \n\toutput_name VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN
KEY(workflow_invocation_step_id) REFERENCES workflow_invocation_step
(id), \n\tFOREIGN KEY(workflow_step_id) REFERENCES workflow_step (id),
\n\tFOREIGN KEY(dataset_collection_id) REFERENCES
history_dataset_collection_association (id)\n)\n\n'] (Background on this
error at: http://sqlalche.me/e/e3q8)


grep  "Warning" FirstRun.log  | cut -f 3,4 -d ":"


Warning: Duplicate index 'ix_galaxy_user_deleted' defined on the table
'galaxydbBGAdev.galaxy_user'. This is deprecated and will be disallowed
in a future release.

Warning: Duplicate index 'ix_galaxy_user_purged' defined on the table
'galaxydbBGAdev.galaxy_user'. This is deprecated and will be disallowed
in a future release.

Warning: Duplicate index 'ix_hdadaa_history_dataset_association_id'
defined on the table
'galaxydbBGAdev.history_dataset_association_display_at_authorization'.
This is deprecated and will be disallowed in a future release.

Warning: Duplicate index 'ix_lddaia_ldda_id' defined on the table
'galaxydbBGAdev.library_dataset_dataset_info_association'. This is
deprecated and will be disallowed in a future release.

Warning: Duplicate index 'ix_hda_ta_history_dataset_association_id'
defined on the table
'galaxydbBGAdev.history_datas

Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

[Hans-Rudolf Hotz]

Dear Martin and Nicola

Thank you very much for your help

Unfortunately, I don't have nodebut manually copying the files seems 
to do the trick.



Regards, Hans-Rudolf



On 06/08/2018 04:48 PM, Martin Čech wrote:

Hi Hans-Rudolf,

the problem is that the 18.05 release is missing the viz static files in
the proper folder. To be precise /config/plugins/visualizations/*/static
needs to be copied to /static/plugins/visualizations/*/static

To fix:

(make sure you have node 8.x.x and not newer)

$ cd client
$ ./node_modules/.bin/gulp plugins

I am sorry for the inconvenience, we will fix this in the release branch
early next week.

Martin







On Fri, Jun 8, 2018 at 10:00 AM Nicola Soranzo mailto:nicola.sora...@gmail.com>> wrote:

Dear Hans-Rudolf,
I think this is being worked on at
https://github.com/galaxyproject/galaxy/pull/6297 .

Cheers,
Nicola

On 08/06/18 14:57, Hans-Rudolf Hotz wrote:
 >
 > just adding a little bit more information:
 >
 >  - this problem happens independent of using paste or uwsgi
 >
 >  - as far as I have tested all visualization plugins (with the
 > exception of trackster) are broken. For broken visualizations, other
 > than 'scatterplot', I get the error: "Load function 'load' not found"
 >
 >
 > Regards,
     > Hans-Rudolf
 >
 >
 > On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:
 >> Hi all
 >>
 >>
 >> I am in the process of upgrading our servers to 18.05. And I have
 >> encountered an issue with the Visualization tool "Scatterplot,
Creates a
 >> 2D-scatterplot from tabular datapoints"
 >>
 >> I am starting with a simple bed file for chromosome 15
(downloaded with
 >> UCSC table browser tool). When I click on the Visualization icon,
 >> followed by "Scatterplot", I end up with an near empty page. I
only get
 >> the title:
 >>
 >> Scatterplot of 'UCSC Main on Human: ncbiRefSeq
 >> (chr15:20010162-22868384)'
 >>
 >> UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)
 >>
 >>
 >>
 >> This happens with our development server (after being upgraded from
 >> 17.09). It is the same using a new clone of 18.05 code.
 >>
 >> It also happens on usegalaxy.eu <http://usegalaxy.eu> but it
does work on usegalaxy.org <http://usegalaxy.org>
 >>
 >>
 >> As a side note: on usegalaxy.org <http://usegalaxy.org>, each
visualization has its little icon
 >> (see: 'usegalaxy.org.png'), while on usegalaxy.eu
<http://usegalaxy.eu>, each visualization
 >> just has an eye (see: 'usegalaxy.eu.png')
 >>
 >>
 >> I hope there is an easy fix for this
 >>
 >>
 >> Regards, Hans-Rudolf
 >>
 >>
 >>
 >>
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 >>
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Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

[Hans-Rudolf Hotz]

just adding a little bit more information:

 - this problem happens independent of using paste or uwsgi

 - as far as I have tested all visualization plugins (with the 
exception of trackster) are broken. For broken visualizations, other 
than 'scatterplot', I get the error: "Load function 'load' not found"



Regards,
Hans-Rudolf


On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote:

Hi all


I am in the process of upgrading our servers to 18.05. And I have
encountered an issue with the Visualization tool "Scatterplot, Creates a
2D-scatterplot from tabular datapoints"

I am starting with a simple bed file for chromosome 15 (downloaded with
UCSC table browser tool). When I click on the Visualization icon,
followed by "Scatterplot", I end up with an near empty page. I only get
the title:

Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)'

UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)



This happens with our development server (after being upgraded from
17.09). It is the same using a new clone of 18.05 code.

It also happens on usegalaxy.eu but it does work on usegalaxy.org


As a side note: on usegalaxy.org, each visualization has its little icon
(see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization
just has an eye (see: 'usegalaxy.eu.png')


I hope there is an easy fix for this


Regards, Hans-Rudolf




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[galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

[Hans-Rudolf Hotz]

Hi all


I am in the process of upgrading our servers to 18.05. And I have 
encountered an issue with the Visualization tool "Scatterplot, Creates a 
2D-scatterplot from tabular datapoints"


I am starting with a simple bed file for chromosome 15 (downloaded with 
UCSC table browser tool). When I click on the Visualization icon, 
followed by "Scatterplot", I end up with an near empty page. I only get 
the title:


Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)'

UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)



This happens with our development server (after being upgraded from 
17.09). It is the same using a new clone of 18.05 code.


It also happens on usegalaxy.eu but it does work on usegalaxy.org


As a side note: on usegalaxy.org, each visualization has its little icon 
(see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization 
just has an eye (see: 'usegalaxy.eu.png')



I hope there is an easy fix for this....


Regards, Hans-Rudolf


--



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Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Galaxy Cleanup

[Hans-Rudolf Hotz]

Hi Christopher


It depends on the setting of "cleanup_job" ('always', 'onsuccess', 
'never'), whether the temporary files are cleaned up or not. Though, to 
be honest, I don't know, if this setting as any influence, when you 
'delete' a job.


For the quotas, only dataset in the histories are counted

The temporary files are very handy for debugging, so I have 'onsuccess' 
on our production server and 'never' on our development server. I just 
regularly check the total size of the working directories and do the 
clean up manually



Regards, Hans-Rudolf




On 04/27/2018 01:51 PM, Previti wrote:

Hi everybody,

I have a hopefully basic questions regarding temporary output files.

A user was generating >4TB output files via the program bedtools
intersectbed. The jobs were cancelled, but I still see the (temporary)
output files that were generated.

Does Galaxy clean these up? Does it do this regularly?

Would a quota prevent something like this from happening again or would
the jobs have to finish before being "counted"?

Thanks and best regards,

Christopher

--
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Genomics and Proteomics Core Facility
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Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work

[Hans-Rudolf Hotz]

Hi Ping


Does it work with a fresh installation ( v17.09) staring with an empty 
PostgrSQL database?



Hans-Rudolf

On 12/19/2017 03:41 PM, Ping Luo wrote:

Hans-Rudolf,

Yes, I have set the flag to be true

 # Allow administrators to log in as other users (useful for debugging)
 allow_user_impersonation = True

We use CAS authentication and our database is Postgresql. Our current
Galaxy is v15.07 and impersonation works well. I have tried v16.10
before and impersonation didn't work either.

Thanks,

Ping

On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Ping

The 'impersonate a user' function works for me with v17.09.


I assume, you have set: "allow_user_impersonation = True" in the
galaxy.ini file?


Do you encounter this problem, for the first time, i.e did it work
before using (v17.05 or earlier) and you only have the issues after
upgrading?

What database do you use?

Do you use external authentication?


Regards, Hans-Rudolf






On 12/18/2017 05:22 PM, Ping Luo wrote:

The impersonation feature in Galaxy v17.09 doesn't work as expected.

After clicking the person to impersonate, the webpage shows "you
have
now logged in as xxx, return to home page', where 'xxx' is the
name of
the person I want to impersonate. So far so good. But after I click
home, and check the login information, the login name is still
myself.

Is there anything I missed in the configuration file?

Thanks,

Ping


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Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work

[Hans-Rudolf Hotz]

Hi Ping

The 'impersonate a user' function works for me with v17.09.


I assume, you have set: "allow_user_impersonation = True" in the 
galaxy.ini file?



Do you encounter this problem, for the first time, i.e did it work 
before using (v17.05 or earlier) and you only have the issues after 
upgrading?


What database do you use?

Do you use external authentication?


Regards, Hans-Rudolf





On 12/18/2017 05:22 PM, Ping Luo wrote:

The impersonation feature in Galaxy v17.09 doesn't work as expected.

After clicking the person to impersonate, the webpage shows "you have
now logged in as xxx, return to home page', where 'xxx' is the name of
the person I want to impersonate. So far so good. But after I click
home, and check the login information, the login name is still myself.

Is there anything I missed in the configuration file?

Thanks,

Ping


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Re: [galaxy-dev] Network errors when downloading files

[Hans-Rudolf Hotz]

Hi Liam

does it happen with every file? on every browser? for every user?

what happens when you try to download a file from usegalaxy.org ?


to me this sounds like an issue with the proxy settings. Something you 
need to discuss with your sys admin


Regards, Hans-Rudolf


On 12/13/2017 09:56 PM, William, Van Der Pol wrote:

Hello,

We’ve noticed when our users try to download files from our galaxy
instance, they are getting a network error and receiving an empty 0 Byte
file. I’ve checked the directory where the datasets are stored and can
see that the files in question exist and contain the expected data, but
something is interfering with downloading them through the GUI.

Do you guys have any suggestions on what could be causing this error?

Thanks

-Liam

*/Help keep the CCTS funded./*/ Please include the following text on
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Re: [galaxy-dev] Dynamic Tool UI based on script

[Hans-Rudolf Hotz]

Sure

However, tools relying on "dynamic_options" and extra "code" scripts are 
usually 'hacks' for accessing external data/services in a local galaxy 
installation. And such tools are not intended for the toolshed 
anywayIMHO.



Hans-Rudolf


On 12/07/2017 09:37 AM, Steve Cassidy wrote:

I could do that but it would mean that no-one could install the tool
from the toolshed without also installing this package.

Maybe I just need to hack this together.

Steve


—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy


On 7 Dec 2017, at 6:59 pm, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Steve

what happened, when you add this module to the environment the galaxy
server is running in? (e.g. by listing the path in the 'run.sh' file)

Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:

Hi all,
  this would help in a tool I’m trying to write too but the problem I
have implementing this approach is that my script will need an external
python module - is there any way that I can list dependencies for the
script?  As it happens these are the same dependancies that the tool
itself will need once executed.

Thanks,

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy


On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:




2017
2016
2015







...


...





The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

  l = os.listdir(rDir)
  p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
  l.sort()
  path = rDir
  filesoptions = [(s) for s in l if os.path.exists(path + s)]
  files = [(s,s,False) for s in filesoptions if p.match(s)]
  return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:

Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e
if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


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Re: [galaxy-dev] Dynamic Tool UI based on script

[Hans-Rudolf Hotz]

Hi Steve

what happened, when you add this module to the environment the galaxy 
server is running in? (e.g. by listing the path in the 'run.sh' file)


Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:

Hi all,
   this would help in a tool I’m trying to write too but the problem I
have implementing this approach is that my script will need an external
python module - is there any way that I can list dependencies for the
script?  As it happens these are the same dependancies that the tool
itself will need once executed.

Thanks,

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy


On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:




 2017
 2016
 2015







...


...





The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

   l = os.listdir(rDir)
   p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
   l.sort()
   path = rDir
   filesoptions = [(s) for s in l if os.path.exists(path + s)]
   files = [(s,s,False) for s in filesoptions if p.match(s)]
   return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:

Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


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Re: [galaxy-dev] Dynamic Tool UI based on script

[Hans-Rudolf Hotz]

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:




  2017
  2016
  2015
 






...


...





The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool 
definition file. The function returns all files with a matching file 
name (i.e.year), and could look like:



rDir = "/data/"

def ds_readFiles(year):

l = os.listdir(rDir)
p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
l.sort()
path = rDir
filesoptions = [(s) for s in l if os.path.exists(path + s)]
files = [(s,s,False) for s in filesoptions if p.match(s)]
return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:

Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


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Re: [galaxy-dev] broken after upgrade to 17.09 : uploading files via the API

[Hans-Rudolf Hotz]

Dear John

Thank you very much for your quick response. Unfortunately, this doesn't 
work for me.


Yes, the dbkey exists. It is not custom build for this user, and other 
datasets already exist in this history with this dbkey.




The culprit is somewhere in the virtual env:


(.venv)-bash-4.2$ which python
/***/galaxy/.venv/bin/python
(.venv)-bash-4.2$
(.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub

=> does not work

...but:

(.venv)-bash-4.2$ /usr/bin/python import_with_dbkey.py *** file.bam hg19sub

=> does work


I can reproduce this without the virtual env (the other way round)


-bash-4.2$ which python
/usr/bin/python
-bash-4.2$
-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub

=> does work

-bash-4.2$ /***/galaxy/.venv/bin/python import_with_dbkey.py *** 
file.bam hg19sub


=> does not work


and if I use the old directory (used with release 17.01)

-bash-4.2$ /***/galaxy_20171120/.venv/bin/python import_with_dbkey.py 
*** file.bam hg19sub


=> it does work as well



Hans-Rudolf



On 11/20/2017 02:02 PM, John Chilton wrote:

Thanks for the report,

I suspect the breaking change would be this -
https://github.com/galaxyproject/galaxy/pull/4563. I added a bunch of
tests for these API changes that I though would ensure backward
compatibility but perhaps there is some sort of breakage here. I
opened a PR in response to this thread against bioblend to ensure
setting the dbkey still works
(https://github.com/galaxyproject/bioblend/pull/252) and it seems to
work for me.

Does that dbkey not properly exist for that user? Maybe there is a
change in behavior for non-existent dbkeys? Or is the dbkey a custom
build for that user? I could write some tests for that if that is the
case.

-John

On Mon, Nov 20, 2017 at 7:38 AM, Hans-Rudolf Hotz  wrote:

Dear All



If I execute the following command:

python import_with_dbkey.py *** file.bam hg19sub

the bam files will be added to the user's history



the code (import_with_dbkey.py) is as follows:

import sys

sys.path.append('***/bioblend-0.10.0-py2.7.egg')
sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg')

from bioblend.galaxy import GalaxyInstance
from bioblend.galaxy.tools import ToolClient

url = "http://galaxy-dev.fmi.ch";
key = "***"

history_id = sys.argv[1]
file_path = sys.argv[2]
dbkey= sys.argv[3]

gi = GalaxyInstance(url=url, key=key)

toolClient = ToolClient(gi)

uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey)



Now, if I use the virtual environment from Galaxy, I get:

(.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub
Traceback (most recent call last):
   File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line 40,
in 
 uploadedFile = toolClient.upload_file(file_path, history_id,
dbkey=dbkey)
   File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py",
line 148, in upload_file
 return self._tool_post(payload, files_attached=True)
   File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py",
line 218, in _tool_post
 return Client._post(self, payload, files_attached=files_attached)
   File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py",
line 171, in _post
 files_attached=files_attached)
   File
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py",
line 131, in make_post_request
 r.status_code, body=r.text)
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:
400: 

400 Bad Request

Bad Request
Your browser sent a request that this server could not understand.



(.venv)-bash-4.2$


...and the file does not get uploaded.


I will continue investigating the difference between the python modules
used, but maybe someone has a clue and could help me


Thank you very much

Hans-Rudolf

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[galaxy-dev] broken after upgrade to 17.09 : uploading files via the API

[Hans-Rudolf Hotz]

Dear All



If I execute the following command:

python import_with_dbkey.py *** file.bam hg19sub

the bam files will be added to the user's history



the code (import_with_dbkey.py) is as follows:

import sys

sys.path.append('***/bioblend-0.10.0-py2.7.egg')
sys.path.append('***/requests_toolbelt-0.7.0-py2.7.egg')

from bioblend.galaxy import GalaxyInstance
from bioblend.galaxy.tools import ToolClient

url = "http://galaxy-dev.fmi.ch";
key = "***"

history_id = sys.argv[1]
file_path = sys.argv[2]
dbkey= sys.argv[3]

gi = GalaxyInstance(url=url, key=key)

toolClient = ToolClient(gi)

uploadedFile = toolClient.upload_file(file_path, history_id, dbkey=dbkey)



Now, if I use the virtual environment from Galaxy, I get:

(.venv)-bash-4.2$ python import_with_dbkey.py *** file.bam hg19sub
Traceback (most recent call last):
  File "/***/galaxy/tools/fmi__api_helpers/import_with_dbkey.py", line 
40, in 
uploadedFile = toolClient.upload_file(file_path, history_id, 
dbkey=dbkey)
  File 
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", 
line 148, in upload_file

return self._tool_post(payload, files_attached=True)
  File 
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/tools/__init__.py", 
line 218, in _tool_post

return Client._post(self, payload, files_attached=files_attached)
  File 
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py", 
line 171, in _post

files_attached=files_attached)
  File 
"/***/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxyclient.py", line 
131, in make_post_request

r.status_code, body=r.text)
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 
400: 


400 Bad Request

Bad Request
Your browser sent a request that this server could not understand.



(.venv)-bash-4.2$


...and the file does not get uploaded.


I will continue investigating the difference between the python modules 
used, but maybe someone has a clue and could help me



Thank you very much

Hans-Rudolf

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Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

[Hans-Rudolf Hotz]

On 10/17/2017 05:02 PM, Matthias Enders wrote:

Hi Hans,

your right, I´ve checked this. The utils are free and the folder on GITHub contains the 
tools needed. Perhaps it´s an idea to change the link on the website 
(https://galaxyproject.org/visualization-setup/) from here 
("http://hgdownload.cse.ucsc.edu/admin/exe/";)
to github? ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils";)


like the whole galaxy project, the Galaxy hub pages are a community 
effort. So feel free to improve the page yourself by making a adding the 
github page as a second resource for the faToTwoBit tool.



Hans-Rudolf




Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht-----
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 16:50
An: Matthias Enders ; 
galaxy-dev@lists.galaxyproject.org
Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol 136, 
Issue 8

Hi Matthias

No, the twobit-files are not mandatory for trackster. They are only required if 
you want to zoom into the nucleotide level.

Also, though, I am not sure, and I recommend to check this with your legal department, 
but I have been under the impression that the tool 'faToTwoBit' can be built from the 
"kent/src/utils" source code directory, which is freely available for all uses, 
isn't-it?


Regards, Hans-Rudolf




On 10/17/2017 04:29 PM, Matthias Enders wrote:

Hi Hans,

actually we are a company and the UCSC Genome Browser is not freely
available for us. As you pinpointed me to the website:
https://galaxyproject.org/visualization-setup/

There is an link to USCS utilities (for creating twobitfiles)
(http://hgdownload.cse.ucsc.edu/admin/exe/)
Actually this tools are also under license agreements, that permits free 
commercial download or usage.

If I understand it correctly the twobit-files are mandatory for trackster, 
implicating that we have to buy licenses for using UCSC Genome Browser and/or 
Trackster?

If yes: Are there any attempts to build in or rebuild this utilities, so the full project 
with all parts "remains" compatible with AFL3 license?

Mit freundlichen Grüßen

Matthias Enders
--
-


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht-
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 10:33
An: Matthias Enders ;
galaxy-dev@lists.galaxyproject.org
Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136,
Issue 8

Hi Matthias

We had a Birds of a Feather session about (the future of) Trackster at the 
recent galaxy community conference in Montpellier. Though, as far as I know (I 
might be wrong), this didn't result in any no active development on the 
Trackster code.

What kind of functionality do you miss? It might be worth rising an issue on 
github (https://github.com/galaxyproject/galaxy/issues) ?


Personally, I consider Trackster and the option to display data at the
UCSC genome browser as two different pairs of shoes:

- Trackster is a easy option to look at your data quickly. It is
particular useful, if you work with non-model organisms

- the display of your data at UCSC is handy, if you want to
visually compare it with all the available UCSC tracks. However, keep
in mind, unless you are using a local copy of the UCSC gemome browser,
the data will leave your local network.



WRT tutorial: Have you seen these pages:

https://galaxyproject.org/learn/visualization/
https://galaxyproject.org/visualization-setup/


Regards, Hans-Rudolf


PS: I took the freedom to change the subject line for easier searching
in the future






On 10/16/2017 03:50 PM, Matthias Enders wrote:

Dear Galaxy Dev List,

we currently searching for a good Genome Browser. As we run a local galaxy instance, we 
noticed the integrated GTB ("Galaxy Track Browser").

So my question is: Is there a roadmap for further support / development of the 
GTB?

Or will it perhaps get replaced/deprecated in the near future (we read a lot of 
UCSC Genome Browser - Galaxy - Integration)?

Another question would be on good sources/tutorials/manuals for configuring and 
setup for the GTB.

Mit freundlichen Grüßen

Matthias Enders
-
--


GERMAN SEED ALLIANCE GmbH

Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

[Hans-Rudolf Hotz]

Hi Matthias

No, the twobit-files are not mandatory for trackster. They are only 
required if you want to zoom into the nucleotide level.


Also, though, I am not sure, and I recommend to check this with your 
legal department, but I have been under the impression that the tool 
'faToTwoBit' can be built from the "kent/src/utils" source code 
directory, which is freely available for all uses, isn't-it?



Regards, Hans-Rudolf




On 10/17/2017 04:29 PM, Matthias Enders wrote:

Hi Hans,

actually we are a company and the UCSC Genome Browser is not freely available 
for us. As you pinpointed me to the website: 
https://galaxyproject.org/visualization-setup/

There is an link to USCS utilities (for creating twobitfiles) 
(http://hgdownload.cse.ucsc.edu/admin/exe/)
Actually this tools are also under license agreements, that permits free 
commercial download or usage.

If I understand it correctly the twobit-files are mandatory for trackster, 
implicating that we have to buy licenses for using UCSC Genome Browser and/or 
Trackster?

If yes: Are there any attempts to build in or rebuild this utilities, so the full project 
with all parts "remains" compatible with AFL3 license?

Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht-
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 10:33
An: Matthias Enders ; 
galaxy-dev@lists.galaxyproject.org
Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Hi Matthias

We had a Birds of a Feather session about (the future of) Trackster at the 
recent galaxy community conference in Montpellier. Though, as far as I know (I 
might be wrong), this didn't result in any no active development on the 
Trackster code.

What kind of functionality do you miss? It might be worth rising an issue on 
github (https://github.com/galaxyproject/galaxy/issues) ?


Personally, I consider Trackster and the option to display data at the
UCSC genome browser as two different pairs of shoes:

   - Trackster is a easy option to look at your data quickly. It is
particular useful, if you work with non-model organisms

   - the display of your data at UCSC is handy, if you want to visually
compare it with all the available UCSC tracks. However, keep in mind,
unless you are using a local copy of the UCSC gemome browser, the data
will leave your local network.



WRT tutorial: Have you seen these pages:

https://galaxyproject.org/learn/visualization/
https://galaxyproject.org/visualization-setup/


Regards, Hans-Rudolf


PS: I took the freedom to change the subject line for easier searching
in the future






On 10/16/2017 03:50 PM, Matthias Enders wrote:

Dear Galaxy Dev List,

we currently searching for a good Genome Browser. As we run a local galaxy instance, we 
noticed the integrated GTB ("Galaxy Track Browser").

So my question is: Is there a roadmap for further support / development of the 
GTB?

Or will it perhaps get replaced/deprecated in the near future (we read a lot of 
UCSC Genome Browser - Galaxy - Integration)?

Another question would be on good sources/tutorials/manuals for configuring and 
setup for the GTB.

Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844
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[galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

[Hans-Rudolf Hotz]

Hi Matthias

We had a Birds of a Feather session about (the future of) Trackster at 
the recent galaxy community conference in Montpellier. Though, as far as 
I know (I might be wrong), this didn't result in any no active 
development on the Trackster code.


What kind of functionality do you miss? It might be worth rising an 
issue on github (https://github.com/galaxyproject/galaxy/issues) ?



Personally, I consider Trackster and the option to display data at the 
UCSC genome browser as two different pairs of shoes:


 - Trackster is a easy option to look at your data quickly. It is 
particular useful, if you work with non-model organisms


 - the display of your data at UCSC is handy, if you want to visually 
compare it with all the available UCSC tracks. However, keep in mind, 
unless you are using a local copy of the UCSC gemome browser, the data 
will leave your local network.




WRT tutorial: Have you seen these pages:

https://galaxyproject.org/learn/visualization/
https://galaxyproject.org/visualization-setup/


Regards, Hans-Rudolf


PS: I took the freedom to change the subject line for easier searching 
in the future







On 10/16/2017 03:50 PM, Matthias Enders wrote:

Dear Galaxy Dev List,

we currently searching for a good Genome Browser. As we run a local galaxy instance, we 
noticed the integrated GTB ("Galaxy Track Browser").

So my question is: Is there a roadmap for further support / development of the 
GTB?

Or will it perhaps get replaced/deprecated in the near future (we read a lot of 
UCSC Genome Browser - Galaxy - Integration)?

Another question would be on good sources/tutorials/manuals for configuring and 
setup for the GTB.

Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844
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Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

[Hans-Rudolf Hotz]

Hi Pavel


what happens if you connect your galaxy instance to an empty PostgreSQL 
database, let galaxy build all the tables and then try to upload files.



Regards, Hans-Rudolf



On 09/22/2017 10:51 AM, Pavel Fibich wrote:

Hello,

do you have any idea why my galaxy 16.07 stop recognizing uploaded files
and format of uploaded files is set to the format 'data'?

After using older version of database backup, galaxy stop recognizing
format of uploaded files (e.g. fasta, fastqc) and everything is set to
format 'data'. Uploaded files are OK, I have tested them on other public
galaxy servers, where they were recognized well. Before changing
database (after the technical problems with the server), recognizing of
the files were OK. Even in debugging level I do not see any errors or
problems in the log (I have compared logs before changing database with
new ones, and there are no differences). From the investigating of
upload.py, I guess something happen with galaxy.datatypes.registry
(settings and code of galaxy were not changed). Do you have any ideas? I
cannot switch the database back and changing file format in Edit
attributes is annoying.

Best, Pavel


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Re: [galaxy-dev] Monitoring Dashboard for Galaxy

[Hans-Rudolf Hotz]

Hi Evan

I assume you are talking about the 'reports' tool?

Have a look here:

https://galaxyproject.org/admin/usage-reports/
https://docs.galaxyproject.org/en/latest/admin/reports.html

Additional (system) information about each executed job can be logged by 
activating plugins in the "./config/job_metrics_conf.xml" file.


https://galaxyproject.org/admin/config/job-metrics/


Hope this helps
Regards, Hans-Rudolf



On 08/17/2017 04:25 PM, evan clark wrote:

I remember there previously being an additional tool that ran on a
different port from galaxy that allowed for monitoring of performance
and jobs running. Is this tool still packaged with galaxy and if so how
can it be activated.
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Re: [galaxy-dev] galaxy-tours : putting the box next to the preview display

[Hans-Rudolf Hotz]

with a little detour via twitter - this is the solution:


  element: "#current-history-panel > ul.list-items > 
div:nth-child(1) .dataset-peek table"



Many Thanks to William Durand for providing the solution!


Hans-Rudolf



On 07/27/2017 12:15 PM, Hans-Rudolf Hotz wrote:

Dear All

I am working on a simple galaxy tour. The galaxy tour builder
(https://github.com/TailorDev/galaxy-tourbuilder) is great and helps a
lot, but unfortunately, not in this particular case:


 - element: "#current-history-panel > ul.list-items >
div:nth-child(1) > div.details > div.actions.clear > div.left >
a.download-btn.icon-btn"
   title: "Download your dataset"
   intro: "You can download every dataset by using the floppy disc
symbol."
   position: "left"


will put the box next to the floppy disc symbol.

What do I have to write as 'element' in order to get the box pointing to
the actual preview data (i.e. the white box)?


Thank you very much for your help
Regards, Hans-Rudolf



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[galaxy-dev] galaxy-tours : putting the box next to the preview display

[Hans-Rudolf Hotz]

Dear All

I am working on a simple galaxy tour. The galaxy tour builder 
(https://github.com/TailorDev/galaxy-tourbuilder) is great and helps a 
lot, but unfortunately, not in this particular case:



- element: "#current-history-panel > ul.list-items > 
div:nth-child(1) > div.details > div.actions.clear > div.left > 
a.download-btn.icon-btn"

  title: "Download your dataset"
  intro: "You can download every dataset by using the floppy disc 
symbol."

  position: "left"


will put the box next to the floppy disc symbol.

What do I have to write as 'element' in order to get the box pointing to 
the actual preview data (i.e. the white box)?



Thank you very much for your help
Regards, Hans-Rudolf


--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Shiny in Galaxy

[Hans-Rudolf Hotz]

Hi Yvan

Yes, after an additional week in the South of France, we traveled back 
safely last weekend.


I use the free version of the shiny server. In addition to what you 
already have mentioned, we run into another 'feature' of the free 
version: you cannot set the R path. You need to set the R path in the 
environment of the user, the shiny server is running as.


I am currently not using IE, since I cannot use Docker in our production 
environment. Hence the detour via an html page linking to the extra 
shiny server. Maybe this will change with Singularity in the future..


Using IE is definitively the way forward.


Regards, Hans-Rudolf




On 07/06/2017 10:58 PM, Yvan Le Bras wrote:

Hi Hans, Hi everyone,

I hope your return trip from GCC has been safe! Unfortunately, I didn't take 
time during gcc to see you Quick and dirty solution... Can we go further on 
this Shiny / Galaxy integration idea ? It seems that the Shiny licence can be a 
problem but it appears to me, if I don't make a mistake, that using the open 
source version of Shiny (without ssl and identification) on Galaxy through IE 
can be sufficent... no ?

Cheers,

Yvan


- Mail d'origine -
De: Hans-Rudolf Hotz 
À: Yvan Le Bras , Md. Rezaul Karim , 
Mohamed Kassam , Timothée VIRGOULAY , Valentin 
CHAMBON 
Cc: Galaxy Dev List 
Envoyé: Mon, 29 May 2017 09:39:10 +0200 (CEST)
Objet: Re: [galaxy-dev] Shiny in Galaxy

Hi Yvan and list

This is great news!

In my limited spare time, I am currently playing with shiny as well. My
current 'quick and dirty' trick goes like this:

The galaxy tool creates a new shiny app and the output of the galaxy
tool is a html page with the URL to the shiny app. I hope, I will have
something ready to show/discuss at GCC


Regards, Hans-Rudolf


On 05/26/2017 04:13 PM, Yvan Le Bras wrote:

Dear Mohamed, Karim, galaxy-dev list,

A rapid e-mail to inform you that we plan to work on this task in the
upcoming weeks with Thimothée and Valentin, copied. We have had some
exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using
the Galaxy "interactive environment" functionality is a good way to
proceed. Don't hesitate to give us more informations to collaborate on
it...

Wishing you a good week end.

Cheers,

Yvan


 Message d'origine 
De : "Md. Rezaul Karim" 
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam 
Cc : Galaxy Dev List 
Objet : Re: [galaxy-dev] Shiny in Galaxy

+1

On May 26, 2017 2:44 PM, "Mohamed Kassam" mailto:k.mam...@gmail.com>> wrote:

 Dear all,

 I have a shiny application working in my RStudio, but I would like
 to integrate it to Galaxy that the users can call my application via
 Galaxy .

 Thanks in Advance,

 Mohamed

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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

On 06/09/2017 03:29 PM, John Chen wrote:

Hans-Rudolf,

That got me past the error, but I i am now having issue authenticating
with against AD, as if its not able to search for the users.  Do I need
a binding service account to search AD object?  Does the bottow 5 lines
look correct?


They look right, but I can't say whether they are correct. You need to 
discuss this with the person who has set up your Active Directory



Hans-Rudolf





cn=galaxy,ou=Security,ou=somegroup,dc=example,dc=org

(&(objectClass=user)(sAMAccountName={username}))
 ADsearchAccount
 AD_Search_Passwrd
 {sAMAccountName}

The logs show that it found the userID and email, but gets an invalid
password on the webportal

galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-09 09:26:34,592
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: email is testuser.n...@example.org
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: username is testUser
galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
authenticate: options are {'bind-user': '{sAMAccountName}',
'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
'allow-register': 'False', 'auto-register-email': '{mail}', 'server':
'ldap://xxx.xxx.xx', 'auto-register': 'True', 'search-base':
'cn=xxx-xx,ou=Security,ou=x xxx,dc=xxx,dc=xx', 'search-filter':
'(&(objectClass=user)(sAMAccountName={username}))',
'auto-register-username': '{sAMAccountName}', 'search-password': '',
'search-user': '', 'bind-password': '{password}'}
galaxy.auth.providers.ldap_ad WARNING 2017-06-09 09:26:34,596 LDAP
authenticate: search returned no results
10.127.220.227 - - [09/Jun/2017:09:26:34 -0400] "POST
/user/login?use_panels=False HTTP/1.1" 200 -
"http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False";
"Mozilla/5.0 (Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101 Firefox/53.0"



*From:* Hans-Rudolf Hotz 
*To:* John Chen ; Galaxy Dev List

*Sent:* Friday, June 9, 2017 3:34 AM
*Subject:* Re: [galaxy-dev] AD Intergration

always keep the mailing list in the loop! in order for others to help or
learn



On 06/08/2017 07:27 PM, John Chen wrote:
 > Hans-Rudolf
 >
 > This is the error I get when I start the Galaxy server.
 >
...
 > xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105
 >

This is very informative. Looking at line 8 in your file:


ldap://ldap.xxx.xx";>ldap://ldap.xxx.xx


The element "a" is not  terminated


What happens, if you try just

ldap://ldap.xxx.xx





Regards, Hans-Rudolf



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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

always keep the mailing list in the loop! in order for others to help or 
learn




On 06/08/2017 07:27 PM, John Chen wrote:

Hans-Rudolf

This is the error I get when I start the Galaxy server.


...

xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105



This is very informative. Looking at line 8 in your file:


href="ldap://ldap.xxx.xx";>ldap://ldap.xxx.xx



The element "a" is not  terminated


What happens, if you try just

ldap://ldap.xxx.xx




Regards, Hans-Rudolf
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Re: [galaxy-dev] AD Intergration

[Hans-Rudolf Hotz]

Hi John



I am trying to integrate AD with Galaxy. My auth_config.xml  look like
the below, but galaxy won't start with those setting.


what error do you get in the log?




 activedirectory


This should be "ldap", shlouldn't-it?



Regards, Hans-Rudolf



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Re: [galaxy-dev] Shiny in Galaxy

[Hans-Rudolf Hotz]

Hi Yvan and list

This is great news!

In my limited spare time, I am currently playing with shiny as well. My 
current 'quick and dirty' trick goes like this:


The galaxy tool creates a new shiny app and the output of the galaxy 
tool is a html page with the URL to the shiny app. I hope, I will have 
something ready to show/discuss at GCC



Regards, Hans-Rudolf


On 05/26/2017 04:13 PM, Yvan Le Bras wrote:

Dear Mohamed, Karim, galaxy-dev list,

A rapid e-mail to inform you that we plan to work on this task in the
upcoming weeks with Thimothée and Valentin, copied. We have had some
exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using
the Galaxy "interactive environment" functionality is a good way to
proceed. Don't hesitate to give us more informations to collaborate on
it...

Wishing you a good week end.

Cheers,

Yvan


 Message d'origine 
De : "Md. Rezaul Karim" 
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam 
Cc : Galaxy Dev List 
Objet : Re: [galaxy-dev] Shiny in Galaxy

+1

On May 26, 2017 2:44 PM, "Mohamed Kassam" mailto:k.mam...@gmail.com>> wrote:

Dear all,

I have a shiny application working in my RStudio, but I would like
to integrate it to Galaxy that the users can call my application via
Galaxy .

Thanks in Advance,

Mohamed

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http://galaxyproject.org/search/ 



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Re: [galaxy-dev] python subprocess OSError when running bwa-mem

[Hans-Rudolf Hotz]

Hi

run.sh

On 05/24/2017 10:51 AM, Georgios Nikolis wrote:

Hi Hans-Rudolf,
many thanks for pointing me to the right direction. samtools was
installed, it was indeed a problem with $PATH.
There are actually path setting scripts provides with the tools, also
for samtools, e.g.
database/dependencies/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f/env.sh
but it seems that they don't get executed automatically on server start.
I did it manually and bwa-mem runs now without errors.
We will have to see whether other tools besides samtools are affected.
Would you recommend that we put such path setting scripts into run.sh?


yes, at least for samtools, I guess this is currently the best option.

Regards, Hans-Rudolf



Best,
Georgios

On 05/22/2017 08:11 AM, Hans-Rudolf Hotz wrote:

Hi Georgios

I am just guessing here, but the error looks familiar:

Do you have samtools installed? and is it in $PATH?
(for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )


Regards, Hans-Rudolf


On 05/19/2017 10:03 AM, Georgios Nikolis wrote:

Dear all,
we are currently working on a new local Galaxy instance (17.01) and we
encounter an error when running bwa-mem jobs. The jobs fail with a
python subprocess OSError triggered in the module
lib/galaxy/datatypes/binary.py
Here is the traceback:

Traceback (most recent call last):
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py",
line 624, in finish_job
 job_state.job_wrapper.finish( stdout, stderr, exit_code )
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350,
in finish
 dataset.datatype.set_meta( dataset, overwrite=False )
   File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line
391, in set_meta
 exit_code = subprocess.call( args=command, stderr=open(
stderr_name, 'wb' ))
   File "/usr/lib64/python2.7/subprocess.py", line 524, in call
 return Popen(*popenargs, **kwargs).wait()
   File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
 errread, errwrite)
   File "/usr/lib64/python2.7/subprocess.py", line 1327, in
_execute_child
 raise child_exception
OSError: [Errno 2] No such file or directory

Has anyone seen this error before? Is there anything we can do to get
rid of it?

Thanks a lot!

Best,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537





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Re: [galaxy-dev] python subprocess OSError when running bwa-mem

[Hans-Rudolf Hotz]

Hi Georgios

I am just guessing here, but the error looks familiar:

Do you have samtools installed? and is it in $PATH?
(for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )


Regards, Hans-Rudolf


On 05/19/2017 10:03 AM, Georgios Nikolis wrote:

Dear all,
we are currently working on a new local Galaxy instance (17.01) and we
encounter an error when running bwa-mem jobs. The jobs fail with a
python subprocess OSError triggered in the module
lib/galaxy/datatypes/binary.py
Here is the traceback:

Traceback (most recent call last):
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 624, in 
finish_job
 job_state.job_wrapper.finish( stdout, stderr, exit_code )
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350, in finish
 dataset.datatype.set_meta( dataset, overwrite=False )
   File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in 
set_meta
 exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' 
))
   File "/usr/lib64/python2.7/subprocess.py", line 524, in call
 return Popen(*popenargs, **kwargs).wait()
   File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
 errread, errwrite)
   File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
 raise child_exception
OSError: [Errno 2] No such file or directory

Has anyone seen this error before? Is there anything we can do to get
rid of it?

Thanks a lot!

Best,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de 
www.dkfz.de 

logo 

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537





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Re: [galaxy-dev] LDAP group data synchronization

[Hans-Rudolf Hotz]

Hi Matthias

This is great! Thank you very much for sharing this with the community.

I hope I will find time to test this with our server soon.


Regards, Hans-Rudolf


On 03/30/2017 01:24 PM, Matthias Bernt wrote:

Dear galaxy-dev,

as a follow-up to my own question I have just implemented a little
python script that syncs groups, group membership and to some extent
also users from a LDAP server to a galaxy server.

I have put this on github:

https://github.com/bernt-matthias/galaxy-group-sync

I would be happy about any comments and suggestions.

Cheers,
Matthias


On 15.03.2017 15:20, Matthias Bernt wrote:

Dear galaxy developers,

I'm currently trying to establish galaxy at the UFZ research center in
Leipzig. I have some questions on how to match the infrastructure of
galaxy and and our local infrastructure. I would be really happy about
some comments on my ideas.

Galaxy external authentication via LDAP is already working -- worked
like a charm :)

How to integrate LDAP group data into galaxy?

My idea would be to regularly sync the groups and user-group
associations from LDAP to galaxy via the API/bioblend.

Adding groups and user-group associations should be no problem, but
how about removing users, groups, or associations? Are there any
pitfalls that I need to consider? How about data associated with deleted
users? Maybe there are already some scripts around that I could build
upon?

Best,
Matthias

P.S. I'm afraid that I ask quite a lot of questions at the moment.
I hope that I will be soon able to contribute a bit.





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Re: [galaxy-dev] deprecated 'page' tag in tool xml - more than deprecated?

[Hans-Rudolf Hotz]

update:


as I am going through all our local tools, I have realized, it has 
nothing to do with the 'page' tag. The problem is somehow related to the 
'dynamic_options' I am sorry for the confusion.


I will probably send you another mail with a different subject later :(


Sorry, Hans-Rudolf



On 03/28/2017 03:59 PM, Hans-Rudolf Hotz wrote:

Dear All

As part of our move to upgrade from v. 16.04 to 17.01, I have noticed
that the 'page' tag in the tool xml file doesn't work anymore.

I know, the 'page' tag has been deprecated for a while, however, we have
many old but important tools where the 'page' tag is in use.

Has the functionality been removed intentionally? Though, I cant find
any comments in the release notes for 16.07,16.10, and 17,01.

Or is there a trick to re-enable it?


Thank you very much for your help
Hans-Rudolf


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[galaxy-dev] deprecated 'page' tag in tool xml - more than deprecated?

[Hans-Rudolf Hotz]

Dear All

As part of our move to upgrade from v. 16.04 to 17.01, I have noticed 
that the 'page' tag in the tool xml file doesn't work anymore.


I know, the 'page' tag has been deprecated for a while, however, we have 
many old but important tools where the 'page' tag is in use.


Has the functionality been removed intentionally? Though, I cant find 
any comments in the release notes for 16.07,16.10, and 17,01.


Or is there a trick to re-enable it?


Thank you very much for your help
Hans-Rudolf

--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

[Hans-Rudolf Hotz]

...and indeed adding it to the "whitelist" 
(~/galaxy_dev/8090/galaxy/lib/galaxy/tools/_init__.py


solves the problem. I can keep 'preserve_python_environment = legacy_only'


I have made a pull request.

Hans-Rudolf

On 03/27/2017 04:38 PM, Hans-Rudolf Hotz wrote:

Hi All

I am in the process of updating our local galaxy servers to release 17.01.

Using the new release, I get the following error, when I try to display
a simple bed file in trackster:


Traceback (most recent call last):
   File
"/***/galaxy_dev/***/galaxy/lib/galaxy/datatypes/converters/interval_to_fli.py",
line 20, in
 from galaxy.datatypes.util.gff_util import
convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf
ImportError: No module named galaxy.datatypes.util.gff_util



When change 'preserve_python_environment = legacy_only' to
'preserve_python_environment = always' in "galaxy.ini" it works.


Looks like more tools need to be added to the "whitelist" ?


Regards, Hans-Rudolf





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[galaxy-dev] Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

[Hans-Rudolf Hotz]

Hi All

I am in the process of updating our local galaxy servers to release 17.01.

Using the new release, I get the following error, when I try to display 
a simple bed file in trackster:



Traceback (most recent call last):
  File 
"/***/galaxy_dev/***/galaxy/lib/galaxy/datatypes/converters/interval_to_fli.py", 
line 20, in
from galaxy.datatypes.util.gff_util import 
convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf

ImportError: No module named galaxy.datatypes.util.gff_util



When change 'preserve_python_environment = legacy_only' to 
'preserve_python_environment = always' in "galaxy.ini" it works.



Looks like more tools need to be added to the "whitelist" ?


Regards, Hans-Rudolf




--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Shared Data Library, large number of files

[Hans-Rudolf Hotz]

this sounds more like a browser issue to me
which browser do you use? what happens when you use a different browser? 
and what happens when you just reload the page



Hans-Rudolf

On 03/01/2017 06:17 PM, D K wrote:

Actually, when I click on the Shared Data-> Data Libraries link I get
only the Galaxy banner and a blank page, so I'm not even seeing the data
libraries themselves.

If I use the Admin link and then click Data libraries, I can see the
actual libraries. But when I try to enter one of the libraries with lots
of files it hangs.


On Wed, Mar 1, 2017 at 9:03 AM, D K mailto:danielforti...@gmail.com>> wrote:

Hi Hans,

I'm running 16.10. If I'm not mistaken, the old Data Library
interface is still accessible in the Admin menu isn't it? I have the
same issue when navigating to a Data Library either from the Admin
or Shared Data links. I also tried this in 16.07 with the same
result.  If it makes a difference, I'm using PostgreSQL and Apache.

Dwight



On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Daniel

Just double checking which version of galaxy are you running? In
other words: are you still using the old Data Library interface?
(if I remember correctly, the old UI was deprecated in 15.10)
We had similar issues with the old UI.

The new one works fine and is very fast. E.g. we have a 'MISEQ'
folder with more than 100 sub folders and a HISEQ folder with
more than 600 sub folders. Each containing up to 100plus fastq
and text files.

Regards, Hans-Rudolf



On 03/01/2017 12:13 AM, D K wrote:

Hi,

I've noticed that the more files / folders (think hundreds
of folders
each with 20+ fastq files) I add to a Shared Data Library,
the longer
and longer it takes to initially navigate the folder
structure (after
clicking on the specific Shared Data Library). Just opening
up the
Shared Data Library can take several minutes and often the
browser times
out. Is there a way to speed this up?

If it's relevant, when I add shared data, it's linked rather
than copied
into Galaxy. Any suggestions would be greatly appreciated

Thanks!


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Re: [galaxy-dev] Shared Data Library, large number of files

[Hans-Rudolf Hotz]

This is bizarre...our production server is on 16.04 and the old UI is no 
longer installed.



On 03/01/2017 06:03 PM, D K wrote:

Hi Hans,

I'm running 16.10. If I'm not mistaken, the old Data Library interface
is still accessible in the Admin menu isn't it? I have the same issue
when navigating to a Data Library either from the Admin or Shared Data
links. I also tried this in 16.07 with the same result.  If it makes a
difference, I'm using PostgreSQL and Apache.

Dwight



On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi Daniel

Just double checking which version of galaxy are you running? In
other words: are you still using the old Data Library interface?
(if I remember correctly, the old UI was deprecated in 15.10)
We had similar issues with the old UI.

The new one works fine and is very fast. E.g. we have a 'MISEQ'
folder with more than 100 sub folders and a HISEQ folder with more
than 600 sub folders. Each containing up to 100plus fastq and text
files.

Regards, Hans-Rudolf



On 03/01/2017 12:13 AM, D K wrote:

Hi,

I've noticed that the more files / folders (think hundreds of
folders
each with 20+ fastq files) I add to a Shared Data Library, the
longer
and longer it takes to initially navigate the folder structure
(after
clicking on the specific Shared Data Library). Just opening up the
Shared Data Library can take several minutes and often the
browser times
out. Is there a way to speed this up?

If it's relevant, when I add shared data, it's linked rather
than copied
into Galaxy. Any suggestions would be greatly appreciated

Thanks!


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Re: [galaxy-dev] Shared Data Library, large number of files

[Hans-Rudolf Hotz]

Hi Daniel

Just double checking which version of galaxy are you running? In other 
words: are you still using the old Data Library interface?

(if I remember correctly, the old UI was deprecated in 15.10)
We had similar issues with the old UI.

The new one works fine and is very fast. E.g. we have a 'MISEQ' folder 
with more than 100 sub folders and a HISEQ folder with more than 600 sub 
folders. Each containing up to 100plus fastq and text files.


Regards, Hans-Rudolf


On 03/01/2017 12:13 AM, D K wrote:

Hi,

I've noticed that the more files / folders (think hundreds of folders
each with 20+ fastq files) I add to a Shared Data Library, the longer
and longer it takes to initially navigate the folder structure (after
clicking on the specific Shared Data Library). Just opening up the
Shared Data Library can take several minutes and often the browser times
out. Is there a way to speed this up?

If it's relevant, when I add shared data, it's linked rather than copied
into Galaxy. Any suggestions would be greatly appreciated

Thanks!


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Re: [galaxy-dev] AD/LDAP Integration

[Hans-Rudolf Hotz]

Hi

I have no solution for you so far. However, I recommend to have a closer 
look at the entries in the 'galaxy_user' table for the users which work, 
and the users which don't work. In particular, check for 'email' and 
'username' whether they are exactly the same as in your accounts provider.


I assume, you have galaxy users, which have been using galaxy before you 
switched to external authentication?


Or have you used authentication through apache before?





Regards, Hans-Rudolf





On 02/02/2017 04:12 PM, Yip, Miu ki wrote:

Hi all,

After setting up AD/LDAP in Galaxy, we noticed that for some reason, some users 
are able to log in but others were not. We don’t think that it has anything to 
do with the set up of LDAP or AD at our institute and we’ve tried to find 
common threads between the users who can log in but we have not found anything 
interesting.

Could someone explain what exactly Galaxy looks for when signing users in with 
AD/LDAP? We found the source code here: ./lib/galaxy/auth/providers/ldap_ad.py 
but all the code seems to be functioning properly.

Here is one of the error outputs in the log when somebody tries to log in for 
the first time, but cannot:

galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authenticate: 
whoami is u:SCIEDU\chess
galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authentication 
successful
server ip - - [01/Feb/2017:17:16:12 -0400] "POST /galaxy/user/login?use_panels=False HTTP/1.0" 200 - 
“http:/galaxyurl.edu/galaxy/user/login?use_panels=False" 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/55.0.2883.95 Safari/537.36"

Exception happened during processing of request from ('127.0.0.1', 55724)
Traceback (most recent call last):
   File 
"/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", 
line 1085, in process_request_in_thread
 self.finish_request(request, client_address)
   File "/usr/lib64/python2.7/SocketServer.py", line 334, in finish_request
 self.RequestHandlerClass(request, client_address, self)
   File "/usr/lib64/python2.7/SocketServer.py", line 651, in __init__
 self.finish()
   File "/usr/lib64/python2.7/SocketServer.py", line 710, in finish
 self.wfile.close()
   File "/usr/lib64/python2.7/socket.py", line 279, in close
 self.flush()
   File "/usr/lib64/python2.7/socket.py", line 303, in flush
 self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe


Any insight would be appreciated. Thanks!
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Re: [galaxy-dev] display at UCSC does not work

[Hans-Rudolf Hotz]

Dear All

I just wanna close this thread and shortly tell you how - with the help 
of Dannon - we solved the problem in the end:


The problem was at our side. Our Galaxy server is not visible from the 
out side. Only requests from the UCSC servers are allowed. Despite the 
claim by our IT department that the requests from UCSC are directly sent 
to our Galaxy server, they are not.


Dannon pointed me to the right position in the the sript:

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/webapp.py

to insert a simple debug statement after line 533, like:

 " print('***',host) "


and this gave me the name of our proxy server. All I had to do was 
adding this name to the list of "UCSC_SERVERS" at the top of the script 
and it worked even when "require_login = True" is set.


With a big Thank You to Dannon Baker!

Regards, Hans-Rudolf





On 09/05/2016 11:44 AM, Hans-Rudolf Hotz wrote:

Hi


I am trying to set up the possibility to display data sets with the UCSC
genome browser for our new galaxy installation.

After clicking on "display at UCSC main", I get the UCSC genome browser,
opening in the right assembly, and at the correct location, but I get
the following Error:

Warning/Error(s):

 redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as



In galaxy.ini, I did uncomment the line:

display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ...


We use the 'new' authentication method to connect to our LDAP server,
with the following changes in galaxy.ini:

require_login = True

auth_config_file = config/auth_conf.xml


Connection from UCSC to our galaxy server is working, since I can
display the data, when I switch to

require_login = False

it works, independent of whether I am logged in or not.



Is there a way to get it to work, even if I have "require_login = True"?


Thank you very much for your help
Regards, Hans-Rudolf






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Re: [galaxy-dev] Connection to mariaDB generates tables, but does not migrate information

[Hans-Rudolf Hotz]

Hi Evan

Although, this is a MySQL to PostgreSQL migration, you might find some 
ideas and tricks for you case as well:


https://wiki.galaxyproject.org/Community/Log/2015/MySQL2PostgreSQL


Regards, Hans-Rudolf


On 12/19/2016 06:46 PM, Nate Coraor wrote:

Hi Evan,

Migration only refers to the schema. Galaxy does not copy data between
databases for you. You'll need to dump the data from your old database
(sqlite?) and load it into the new one. We don't have instructions for
this but most general guides for this conversion available on the web
should get you started.

Thanks,
--nate

On Mon, Dec 19, 2016 at 12:26 PM, evan clark mailto:eclar...@fau.edu>> wrote:

I connected our galaxy instance to mariadb with no connection issues
and it began to migrate the data, I noticed however when galaxy was
finally started the tables were generated, but no data was migrated.
It completed the migration without error so I am not sure if there
is a setting I missed in mariadb.
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[galaxy-dev] MySQL versus PostgreSQL - was: History is not accessible by user

[Hans-Rudolf Hotz]

On 12/01/2016 12:08 PM, Maximilian Friedersdorff wrote:




>PS: and a completely unrelated piece of advice: Once you have fixed
>this issue, I strongly recommend switching to PostgreSQL.

>

I gather SQLAlchemy prefers this!  What kind of issues can I expect when
using MySQL?



As far as I am aware, there are no current (unsolvable) issues with 
MySQL. Since all the development is done with PostgreSQL, this might 
change in the future.


Hans-Rudolf
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Re: [galaxy-dev] Datasets incorrectly flagged as deleted

[Hans-Rudolf Hotz]

Hi Lance


I don't remember seeing the problem you describe with our servers. If I 
do your query, I get:


...
 count
---
55
(1 row)


looking at the actual ids, they are all in the lower three digits range 
and many years old.


Regards, Hans-Rudolf




On 11/30/2016 08:20 PM, Lance Parsons wrote:

I've run into issues over the past year where some jobs would
occasionally fail to start (stuck in a `new` state). I tracked them down
to a situataion where `dataset.deleted` is set to `t` yet the
`history_dataset_association.deleted` is `f`. Simply setting
`dataset.deleted` to `f` in those instances resolved the issue and the
jobs ran. The datasets have all still been on disk.

Since this is a pretty annoying situation, I thought I'd check to see if
there are other datasets with this problem. Shockingly, I found many
thousands of such datasets:

```
select count(d.id)
 from dataset d
 join history_dataset_association hda on d.id = hda.dataset_id
 where d.deleted = 't' and hda.deleted = 'f';
  count
---
  76977
(1 row)
```

I'm hesitant to update so many rows in my database so I thought I'd put
this out there for comment. What do others see when running the above
query? Has anyone run into this or a similar issue? Thanks.


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Re: [galaxy-dev] History is not accessible by user

[Hans-Rudolf Hotz]

Hi Max

This does look bizarre indeed. I have no answer, and I can just 
recommend a few things to test:



- delete your cookies

- how do you authenticate your users? can you log in as someone else? 
what happens if you set 'require_login = False'


- what happens if you simplify your installation: i.e. switch back to 
the built in SQlite database



Regards, Hans-Rudolf

PS: and a completely unrelated piece of advice: Once you have fixed 
this issue, I strongly recommend switching to PostgreSQL.







On 11/30/2016 05:25 PM, Maximilian Friedersdorff wrote:




Hi,

I'm currently trying to install a galaxy instance for production.
Eventually that will involve proxying through apache but for the moment
I'm testing by accessinghttp://localhost:8080  directly.

When I load the front page, I get the following error:

{
   "agent": "Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 
Firefox/45.0",
   
"url":"http://localhost:8080/galax/galaxy/api/histories/1cd8e2f6b131e891?keys=size%2Cnon_ready_jobs";,
   "options": {
 "parse": true,
 "data": "keys=size%2Cnon_ready_jobs",
 "emulateHTTP": false,
 "emulateJSON": false,
 "textStatus": "error",
 "errorThrown": "Forbidden"
   },
   "xhr": {
 "readyState": 4,
 "responseText": "{\"err_msg\": \"History is not accessible by user\", 
\"err_code\": 403002}",
 "responseJSON": {
   "err_msg": "History is not accessible by user",
   "err_code": 403002
 },
 "status": 403,
 "statusText": "Forbidden",
 "responseHeaders": {
   "Server": "PasteWSGIServer/0.5 Python/2.7.5\r",
   "Date": "Wed, 30 Nov 2016 16:17:11 GMT\r",
   "x-frame-options": "SAMEORIGIN\r",
   "Content-Type": "application/json\r",
   "Cache-Control": "max-age=0,no-cache,no-store\r",
   "Connection": "close\r"
 }
   },
   "source": {
 "model_class": "History",
 "id": "1cd8e2f6b131e891",
 "name": "Unnamed history",
 "state": "new",
 "deleted": false,
 "importable": false,
 "create_time": "2016-11-30T16:17:11",
 "contents_url": "/galaxy/api/histories/1cd8e2f6b131e891/contents",
 "size": 0,
 "user_id": null,
 "username_and_slug": null,
 "annotation": null,
 "state_details": {
   "paused": 0,
   "ok": 0,
   "failed_metadata": 0,
   "upload": 0,
   "discarded": 0,
   "running": 0,
   "setting_metadata": 0,
   "error": 0,
   "new": 0,
   "queued": 0,
   "empty": 0
 },
 "empty": true,
 "update_time": "2016-11-30T16:17:11",
 "tags": [],
 "genome_build": "?",
 "slug": null,
 "url": "/galaxy/api/histories/1cd8e2f6b131e891",
 "state_ids": {
   "paused": [],
   "ok": [],
   "failed_metadata": [],
   "upload": [],
   "discarded": [],
   "running": [],
   "setting_metadata": [],
   "error": [],
   "new": [],
   "queued": [],
   "empty": []
 },
 "published": false,
 "purged": false,
 "nice_size": "0 b"
   },
   "user": {
 "id": null,
 "username": "(anonymous user)",
 "email": "",
 "total_disk_usage": 0,
 "nice_total_disk_usage": "0 bytes",
 "quota_percent": null,
 "is_admin": false
   }
}


I'm not sure what to make of that.

Galaxy is running as it's own user and group, in a subdirectory of the
home directory of that user.  File permissions are sufficiently
permissive.  It is connecting to a mysql database `galaxy' as a user
that has ALL PRIVILEGES on `galaxy'.* tables.

It is galaxy version 16.07, running on CentOS7.2 if it matters.

I've been battling with SELinux to give apache sufficient permissions to
act as a proxy for galaxy, but this issue is (I think) separate from that.

Thanks

Max

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Re: [galaxy-dev] Moving Galaxy Install From One Server To Another

[Hans-Rudolf Hotz]

Hi Evan

Well, in theory, this is a simple task, since Galaxy mostly works with 
relative paths. Of course, it all depends on how sophisticated your 
installation is and how different the old and the new 'machine' is (eg 
same OS?)


So my advice is: just do it or rather try it.

 - make a copy of your installation on the new hardware (at first it is 
sufficient to copy only the latest sub directories of database/files/)


 - make a copy of your PostgreSQL database

 - connect your copied installation to the PostgreSQL database copy and 
test, and test, and test


 - pay special attention to tools you have installed via the toolshed. 
You might need to change some absolute paths in the 'env.sh' files 
located in the tool_dependencies/ directory.



Once your happy with all the tests, do an rsync on the database/ 
directory and connect to the original PostgreSQL database.



Regards, Hans-Rudolf




On 11/22/2016 07:52 PM, evan clark wrote:

Is there a good method for moving a fully functional galaxy install from
one machine to another in a different directory?
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Re: [galaxy-dev] Budgeting a production Galaxy instance

[Hans-Rudolf Hotz]

Hi Vladimir

It is difficult to give you a good number, as it depends on a lot of 
factors, like:


 - how "active" are your anticipated '50 active user'? more than 1 
job/workflow a day or just 1 job/workflow a month?


 - do you have to set up a system in order to give the galaxy users 
access to 'external' data, like fastq files?


 - how much training and what kind of training will they need

 - what kind of tools do you wanna integrate and/or write

 - do you have an IT-department which will help you, or do you have to 
do all the sysadmin stuff for the cluster as well



To start, I would recommend at least two full time positions. This will 
give you enough manpower to set up the instance and provide training in 
the initial phase. And later, you will have enough flexibility to 
integrate new tools, follow the developments in the wider galaxy 
universe...and eventually give something back to the galaxy community.




Regards, Hans-Rudolf


On 10/05/2016 10:55 PM, Vladimir Gritsenko wrote:

Hello all,

We (at Tel Aviv University) are considering setting up a Galaxy instance 
(private, but production-geared). The capacity planning pages and surveys are 
great for hardware budgeting, but I want to ask about manpower. We’re looking 
forward to roughly 50 active users, and we’ll need to provide troubleshooting, 
training and integrating and writing new tools. In your experience, what is be 
the scope of a Galaxy admin’s position? Part-time? Full-time? Something else? 
Is more than one person needed to handle everything?

Thank you,
Vladimir Gritsenko
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Re: [galaxy-dev] Odd error, solution not understood

[Hans-Rudolf Hotz]

Hi Scott

click on the question mark next to 'database' in your history item and 
set the "Database/Build" to the genome you need.



Regards, Hans-Rudolf

On 09/13/2016 09:11 PM, Scott Szakonyi wrote:

Hi all,

I'm getting the following error when attempting to do a trackster
visualization:

Error: The requested genome file 
(/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be 
opened. Exiting!
Couldn't open 
/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len

I found a discussion related to this error online at
https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered
solution actually means in terms of what I need to do. It says "
You'll need to set your dataset's database/dbkey to your custom
reference genome before you can visualize it". Can someone point me in
the right direction to solve this issue?

Thanks in advance,

Scott

--
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu 


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Re: [galaxy-dev] Converting an internal user to an external user

[Hans-Rudolf Hotz]

Hi Ryan

Are you doing external authentication via apache?

if so, I suggest to change the value in the 'external' column from 'f' 
to 't' in the galaxy_user table.


also, check, whether the e-mail used is really the same as the one 
coming from your external authentication system.


However, be very careful, whenever you manually interact with the Galaxy 
PostgreSQL database. Make sure you have an up-to-date back-up.


Hope this helps,
Hans-Rudolf



On 09/07/2016 05:27 PM, Ryan G wrote:

Hi all - I'm having a problem with a user account and Galaxy getting
confused with it being internal vs external.

When we first set up galaxy, we were using Galaxy's internal
authentication system.  This worked well but all our users then had
another password to keep track of.

We activated external user authentication a few months ago and it works
fine for us.

This user hasn't logged in since and recently tried but is unable to.

I discovered her account in Galaxy appears as an internal account eg
created before we were using external authentication.   Now that we have
external authentication, Galaxy doesn't recognize her and she gets the
user_disabled page whenever she tries to log in.

Is there a way I can change her account in Galaxy from being an internal
to an external account?

Ryan


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[galaxy-dev] display at UCSC does not work

[Hans-Rudolf Hotz]

Hi


I am trying to set up the possibility to display data sets with the UCSC 
genome browser for our new galaxy installation.


After clicking on "display at UCSC main", I get the UCSC genome browser, 
opening in the right assembly, and at the correct location, but I get 
the following Error:


Warning/Error(s):

redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as



In galaxy.ini, I did uncomment the line:

display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ...


We use the 'new' authentication method to connect to our LDAP server, 
with the following changes in galaxy.ini:


require_login = True

auth_config_file = config/auth_conf.xml


Connection from UCSC to our galaxy server is working, since I can 
display the data, when I switch to


require_login = False

it works, independent of whether I am logged in or not.



Is there a way to get it to work, even if I have "require_login = True"?


Thank you very much for your help
Regards, Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Docker on Windows 10

[Hans-Rudolf Hotz]

Hi Jochen

I would definitively go for the native docker for Windows and not using 
docker tool box. Though, this is based on my experience using native 
docker for Mac versus docker tool box.


Maybe someone else on the list has experience with running Bjoern's 
docker images on windows?



Yes, once you get the '-v' option running, it will be possible to modify 
galaxy files and keep the changes.


Hans-Rudolf

On 08/31/2016 01:56 PM, Jochen Bick wrote:

Hi Hans-Rudolf,

thanks for the quick reply.


docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/
bgruening/galaxy-stable /bin/bash


this looks really nice. Is it possible to modify galaxy files in the
interactive session or will it all be reseted after closing the session?



This will provide an interactive session. You can then start Galaxy (and
other stuff like the required PostgreSQL server) with

startup > log 2>&1 &


the startup takes quite a long time and also shows a lot of errors like:
could not connect to server: Connection refused
  Is the server running on host "localhost" (127.0.0.1) and accepting
  tcp/ip connections on port 5432?

and its not running.




and have access to the container.


with regard to using the '-v' option: are you using the native docker
for Windows or are you using the docker tool box?


I'm using native docker for Windows. is there any benefit using docker
tool box?

Best Jochen

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Re: [galaxy-dev] Docker on Windows 10

[Hans-Rudolf Hotz]

Hi Jochen

try starting docker with:

docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ 
bgruening/galaxy-stable /bin/bash


This will provide an interactive session. You can then start Galaxy (and 
other stuff like the required PostgreSQL server) with


startup > log 2>&1 &

and have access to the container.


with regard to using the '-v' option: are you using the native docker 
for Windows or are you using the docker tool box?



Regards, Hans-Rudolf



On 08/30/2016 10:07 PM, Jochen Bick wrote:

Hi,

I am on the way to set up a Docker container on win 10. My problem is
that I do not often work on win 10. My idea is to set up a galaxy which
can be uses once in a while if needed and will be shutdown or not
started if not needed:
So I am interested in exporting all datasets including the database. In
addition I would like to install tools from the toolshed which will be
kept after restarting the docker.

So ware I did the following:
docker run -d -p 8080:80 -v E:\galaxy_storage\:/export/
bgruening/galaxy-stable

its running but there are no files appearing at E:\galaxy_storage\

is it also possible to modify the galaxy.ini?

or to ssh to the docker container?

Thanks in advance Jochen
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Re: [galaxy-dev] how to create users through Galaxy API?

[Hans-Rudolf Hotz]

Hi Peter

I guess it is here:

https://docs.galaxyproject.org/en/master/api_doc.html


Regards,  Hans-Rudolf

On 08/29/2016 05:27 PM, Peter Cock wrote:

Hi Martin,

I'd like to look into creating new users via the API (where we can
control the email address and username format for integration with our
cluster), and have the web-interface forbid users from self-registration.

The read-the-docs site you mentioned in this old email (below) doesn't
exist anymore, and the API wiki page doesn't seem to link to something
similar:

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

Where is the official API documentation now?

Thanks,

Peter

On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech mailto:mar...@bx.psu.edu>> wrote:

Hi,

you specify username, password and email in the body (payload) of
the POST as Key:Value pairs.

Code from the API method: (

https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create


)


username=payload['username']email=payload['email']password=payload['password']

There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find
these when you look at the source code of the method (because the
documentation is not perfect yet, sorry).

M.




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Re: [galaxy-dev] Galaxy migration to docker environment

[Hans-Rudolf Hotz]

Hi Matthias

You don't need to change the path. All data sets are stored in relative 
paths in the PostgreSQL database.


Hence, in a setup without local modifications all you need to do:
 - copy the 'database/files/' folder
 - make sure your new Galaxy installation points to the old PostgreSQL 
database.



Hans-Rudolf


On 08/29/2016 12:02 PM, Matthias De Smet wrote:


Hi all,

We’re looking to migrate our Galaxy instance from a VM based solution to a 
docker based solution. Therefore, we need to move all our user and reference 
data. What is the best possible solution to migrate all data and change the 
path of said data in the database?

Thanks!
M


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Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

[Hans-Rudolf Hotz]

Hi John and Nicola

Thank you very much for working on this and presenting a solution so fast!

Hans-Rudolf

PS: https://github.com/galaxyproject/galaxy/pull/2800


On 08/16/2016 04:40 PM, John Chilton wrote:

Yup - thanks for the bug report. I have used your rna example to build
a minimal-ish example to fit into Galaxy's test tools framework here
https://github.com/galaxyproject/galaxy/pull/2795. I also tested in
16.01 and it worked - so this clearly broke in 16.04. I'll see if I
can track it down and we can move the discussion to the github PR.
Thanks a bunch for the detailed report Hans!

-John

On Tue, Aug 16, 2016 at 9:02 AM, Hans-Rudolf Hotz  wrote:

Hi Nicola and others on the list

It looks like it has something to do with the 'conditional'

I took the rnaStar xml file, and reduced it to the bare bones, just to
reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It
picks up the right dbkey.

I made the xml file even simpler and removed the  'conditional' (see
attachment: rg_rnaStar.simple_noCond  ). And now it no longer works (see
attached screenshot)

And just for completeness: There is nothing in the logs


However, if I use the same two xml files on our current galaxy servers
(running 15.10). It works in both cases. Each time, the right dbkey is
picked up.


  Hans-Rudolf




On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote:


Hi Nicola

Many thanks for your comments/suggestions. I've just tested the rnaStar
wrapper, and it works as well.

I will try to dig deeper

Hans-Rudolf




On 08/16/2016 01:38 PM, Nicola Soranzo wrote:


I've tested bowtie_wrapper on Galaxy release_16.04: 
works fine for me.

Cheers,
Nicola

On 16/08/16 11:42, Nicola Soranzo wrote:


Forget about my previous comment, I should have read your email
better, sorry!

Your code similar to bowtie_wrapper is also used by

https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml

and I think it should work, not sure if it's a regression in Galaxy.

Cheers,
Nicola

On 16/08/16 11:29, Nicola Soranzo wrote:


Hi Hans,
see my comment below.

On 16/08/16 09:51, Hans-Rudolf Hotz wrote:


Dear All


I am trying to move our Galaxy installation to new hardware and at
the same time to a new version (the original is "15.10",minor
version "2" via mercurial; the new is "16.04" via github):

So far, I am making good progress, but I am struggling with a tool
which was written by someone else who has left more than 2 years
ago. The problem is: it doesn't set the dbkey correctly.

I get:




The tool xml is as follows:





   


...



   
  
 



It seems you are missing a param_attribute="dbkey" here, it should be:


Cheers,
Nicola



   





The user can select a genome (based on the Bioconductor BSgenome
packages) from the tab delimited fmi__quasr_genomes table, which
looks like:

hg19BSghg19BSgBSgenome Hsapiens (UCSC hg19)
BSgenome.Hsapiens.UCSC.hg19
hg18BSghg18BSgBSgenome Hsapiens (UCSC hg18)
BSgenome.Hsapiens.UCSC.hg18
ce10BSgce10BSgBSgenome Celegans (UCSC ce10)
BSgenome.Celegans.UCSC.ce10
ce6BSgce6BSgBSgenome Celegans (UCSC ce6)
BSgenome.Celegans.UCSC.ce6
...


The tool works:
  - it displays the available genomes (BSgenome Hsapiens (UCSC hg19),
hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc)
  - once the job is submitted, it uses the right Bioconductor package
(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc)

However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get:




Has anything changed with the 'action' tag since release 15.10?
which makes this simple xml no longer working?

I have to admit, it does look different than the example on the wiki

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

). I tried the code from the wiki which is based on the
bowtie_wrapper

(https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml)

as well:


   
   
   
  
  
   
 
   


but it results in the same kind of error:



Thank you very much for any help/comments

Regards, Hans-Rudolf









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Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

[Hans-Rudolf Hotz]

Hi Nicola and others on the list

It looks like it has something to do with the 'conditional'

I took the rnaStar xml file, and reduced it to the bare bones, just to 
reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It 
picks up the right dbkey.


I made the xml file even simpler and removed the  'conditional' (see 
attachment: rg_rnaStar.simple_noCond  ). And now it no longer works (see 
attached screenshot)


And just for completeness: There is nothing in the logs


However, if I use the same two xml files on our current galaxy servers 
(running 15.10). It works in both cases. Each time, the right dbkey is 
picked up.



 Hans-Rudolf



On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote:

Hi Nicola

Many thanks for your comments/suggestions. I've just tested the rnaStar
wrapper, and it works as well.

I will try to dig deeper

Hans-Rudolf




On 08/16/2016 01:38 PM, Nicola Soranzo wrote:

I've tested bowtie_wrapper on Galaxy release_16.04: 
works fine for me.

Cheers,
Nicola

On 16/08/16 11:42, Nicola Soranzo wrote:

Forget about my previous comment, I should have read your email
better, sorry!

Your code similar to bowtie_wrapper is also used by
https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml

and I think it should work, not sure if it's a regression in Galaxy.

Cheers,
Nicola

On 16/08/16 11:29, Nicola Soranzo wrote:

Hi Hans,
see my comment below.

On 16/08/16 09:51, Hans-Rudolf Hotz wrote:

Dear All


I am trying to move our Galaxy installation to new hardware and at
the same time to a new version (the original is "15.10",minor
version "2" via mercurial; the new is "16.04" via github):

So far, I am making good progress, but I am struggling with a tool
which was written by someone else who has left more than 2 years
ago. The problem is: it doesn't set the dbkey correctly.

I get:




The tool xml is as follows:


   
   
   
  
   

...


   
  
 



It seems you are missing a param_attribute="dbkey" here, it should be:


Cheers,
Nicola



  
   




The user can select a genome (based on the Bioconductor BSgenome
packages) from the tab delimited fmi__quasr_genomes table, which
looks like:

hg19BSghg19BSgBSgenome Hsapiens (UCSC hg19)
BSgenome.Hsapiens.UCSC.hg19
hg18BSghg18BSgBSgenome Hsapiens (UCSC hg18)
BSgenome.Hsapiens.UCSC.hg18
ce10BSgce10BSgBSgenome Celegans (UCSC ce10)
BSgenome.Celegans.UCSC.ce10
ce6BSgce6BSgBSgenome Celegans (UCSC ce6)
BSgenome.Celegans.UCSC.ce6
...


The tool works:
 - it displays the available genomes (BSgenome Hsapiens (UCSC hg19),
hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc)
 - once the job is submitted, it uses the right Bioconductor package
(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc)

However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get:




Has anything changed with the 'action' tag since release 15.10?
which makes this simple xml no longer working?

I have to admit, it does look different than the example on the wiki
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set

). I tried the code from the wiki which is based on the
bowtie_wrapper
(https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml)

as well:


  
  
  
 
 
  

  


but it results in the same kind of error:



Thank you very much for any help/comments

Regards, Hans-Rudolf









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Gapped-read mapper for RNA-seq data
echo foo > $mapped_reads

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

[Hans-Rudolf Hotz]

Hi Nicola

Many thanks for your comments/suggestions. I've just tested the rnaStar 
wrapper, and it works as well.


I will try to dig deeper

Hans-Rudolf




On 08/16/2016 01:38 PM, Nicola Soranzo wrote:

I've tested bowtie_wrapper on Galaxy release_16.04: 
works fine for me.

Cheers,
Nicola

On 16/08/16 11:42, Nicola Soranzo wrote:

Forget about my previous comment, I should have read your email
better, sorry!

Your code similar to bowtie_wrapper is also used by
https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml
and I think it should work, not sure if it's a regression in Galaxy.

Cheers,
Nicola

On 16/08/16 11:29, Nicola Soranzo wrote:

Hi Hans,
see my comment below.

On 16/08/16 09:51, Hans-Rudolf Hotz wrote:

Dear All


I am trying to move our Galaxy installation to new hardware and at
the same time to a new version (the original is "15.10",minor
version "2" via mercurial; the new is "16.04" via github):

So far, I am making good progress, but I am struggling with a tool
which was written by someone else who has left more than 2 years
ago. The problem is: it doesn't set the dbkey correctly.

I get:




The tool xml is as follows:


   
   
   
  
   

...


   
  
 



It seems you are missing a param_attribute="dbkey" here, it should be:


Cheers,
Nicola



  
   




The user can select a genome (based on the Bioconductor BSgenome
packages) from the tab delimited fmi__quasr_genomes table, which
looks like:

hg19BSghg19BSgBSgenome Hsapiens (UCSC hg19)
BSgenome.Hsapiens.UCSC.hg19
hg18BSghg18BSgBSgenome Hsapiens (UCSC hg18)
BSgenome.Hsapiens.UCSC.hg18
ce10BSgce10BSgBSgenome Celegans (UCSC ce10)
BSgenome.Celegans.UCSC.ce10
ce6BSgce6BSgBSgenome Celegans (UCSC ce6)
BSgenome.Celegans.UCSC.ce6
...


The tool works:
 - it displays the available genomes (BSgenome Hsapiens (UCSC hg19),
hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc)
 - once the job is submitted, it uses the right Bioconductor package
(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc)

However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get:




Has anything changed with the 'action' tag since release 15.10?
which makes this simple xml no longer working?

I have to admit, it does look different than the example on the wiki
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set
). I tried the code from the wiki which is based on the
bowtie_wrapper
(https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml)
as well:


  
  
  
 
 
  

  


but it results in the same kind of error:



Thank you very much for any help/comments

Regards, Hans-Rudolf









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[galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

[Hans-Rudolf Hotz]

Dear All


I am trying to move our Galaxy installation to new hardware and at the 
same time to a new version (the original is "15.10",minor version "2" 
via mercurial; the new is "16.04" via github):


So far, I am making good progress, but I am struggling with a tool which 
was written by someone else who has left more than 2 years ago. The 
problem is: it doesn't set the dbkey correctly.


I get:




The tool xml is as follows:


   format="qsamples,qsamplespaired" label="Sample File" help="set of 
sequence files created by the 'select sequence files' tool">

   
   

  
   

...


   

  
 

 
  
   




The user can select a genome (based on the Bioconductor BSgenome 
packages) from the tab delimited fmi__quasr_genomes table, which looks like:


hg19BSg hg19BSg BSgenome Hsapiens (UCSC hg19)   BSgenome.Hsapiens.UCSC.hg19
hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18)   BSgenome.Hsapiens.UCSC.hg18
ce10BSg ce10BSg BSgenome Celegans (UCSC ce10)   BSgenome.Celegans.UCSC.ce10
ce6BSg  ce6BSg  BSgenome Celegans (UCSC ce6)BSgenome.Celegans.UCSC.ce6
...


The tool works:
 - it displays the available genomes (BSgenome Hsapiens (UCSC hg19), 
hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc)
 - once the job is submitted, it uses the right Bioconductor package 
(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc)


However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get:




Has anything changed with the 'action' tag since release 15.10? which 
makes this simple xml no longer working?


I have to admit, it does look different than the example on the wiki 
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set 
). I tried the code from the wiki which is based on the bowtie_wrapper 
(https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml) 
as well:



  

  column="1" offset="0">
 compare="startswith" keep="False"/>

 
 
    
  


but it results in the same kind of error:



Thank you very much for any help/comments

Regards, Hans-Rudolf







--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Removing job in error state

[Hans-Rudolf Hotz]

Hi Ryan

If the "Stop Jobs" option on the Admin page does not work, you can go 
for the direct way by manually interacting with the PostgreSQL database:


Change the state to "error"  in the 'job' table, eg:

update job set state='error' where id=12772;


As always, be very careful when you directly access the PostgreSQL 
database! Make sure your database is properly backed up. And you should 
only consider this as the very last option.



Hans-Rudolf


On 08/04/2016 06:02 AM, Ryan G wrote:

Hi - In the Manage Jobs admin job, I have a job from a user that never
ran successfully.   It shows:
Job ID  UserLast Update ToolState   Inputs  Command LineJob 
Runner
PID/Cluster ID
12772   u...@company.com 654 hours ago
cshl_fastx_collapsernew 13653 error NoneNoneNone


How do I remove this job?  I can't find a way to delete it.


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Re: [galaxy-dev] Galaxy history UI suggestion

[Hans-Rudolf Hotz]

Hi Bongsoo

The 'View all histories' tool (the function to the right of the 'History 
options' wheel) is a good alternative to the 'Saved Histories' page.



Regards, Hans-Rudolf


On 08/02/2016 10:26 PM, Bongsoo Park wrote:

Hello,

In the saved histories, the selected page goes to the first page all the
times. I think it is not convenient. Let's say I want to browse the
histories in page 17. (maybe 20 histories are there). I had to click
again the page 17 (button navigation) if I want to browse another
history in page 17. It would be great someone can enhance this UI issue
(user experience). Thanks!

Best,
Bongsoo


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Re: [galaxy-dev] This job failed for reasons that could not be determined.

[Hans-Rudolf Hotz]

Hi Ulf


I don't think the two things are connected which each other. In the logs 
of our local installation we see once in a while, lines like:



  File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe

but without any errors or failed jobs associated. We consider those as 
harmless, temporary glitches in the web server part of galaxy.


Sorry, not much help...


Just one question for clarification, which might help others (with more 
cloud experience) to jump in: do the failed jobs occur randomly with any 
tool? or are they all coming from the same tool?



Regards, Hans-Rudolf




On 07/25/2016 12:48 PM, Ulf Schaefer wrote:

Hi all

Certain jobs fail on my cloud Galaxy instance with the error message in
the subject line. No stderr or stdout is produced by the tool, at least
it's not accessible from Galaxy. However the data seems to be there, in
so far that I can view it (clicking on the eye) and download it using
the floppy disk icon.

The only thing I see (repeatedly) in my Galaxy logs is this:


Exception happened during processing of request from ('127.0.0.1', 46619)
Traceback (most recent call last):
 File
"/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1085, in process_request_in_thread
   self.finish_request(request, client_address)
 File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
   self.RequestHandlerClass(request, client_address, self)
 File "/usr/lib/python2.7/SocketServer.py", line 657, in __init__
   self.finish()
 File "/usr/lib/python2.7/SocketServer.py", line 716, in finish
   self.wfile.close()
 File "/usr/lib/python2.7/socket.py", line 283, in close
   self.flush()
 File "/usr/lib/python2.7/socket.py", line 307, in flush
   self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe


Does this look familiar to anyone?

Thanks very much for any input
Ulf

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Re: [galaxy-dev] switching from Apache to "auth_conf" to handle external user authentication via LDAP

[Hans-Rudolf Hotz]

Hi John

Thanks for your reply.

I will do some more test, and then add a comment in the wiki


Hans-Rudolf




On 07/25/2016 03:05 PM, John Chilton wrote:

I can't confirm it is going to work without negative repercussions - I
can only say that I cannot think of any non-obvious problems that
would result from doing this. It seems like it is going to be the
right thing to do in your case (but no promises :)).

If it works, it would be super awesome if you update the wiki - thanks
for taking the time to do that!

-John


On Mon, Jul 25, 2016 at 9:00 AM, Hans-Rudolf Hotz  wrote:

Dear all


Our production server uses Apache to handle external user authentication.

I have now set up a new test server (16.04) which handles external user
authentication via LDAP using the auth_conf file. This works nicely when
using an empty database (I have managed to solve all last weeks problems).


I have now connected my test server to a copy of the PostgreSQL database
used on our production server. I try to log in, and I get:

"This account was created for use with an external authentication method,
contact...)

and the login fails.


If I now set external = 'f'  in the galaxy_user table, it works


Since manually modifying the database is a bad thing, I just want to double
check, whether this is the right way to do it?


If so, I will add a line or two to the wiki


Many thanks for your help
Hans-Rudolf



--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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[galaxy-dev] switching from Apache to "auth_conf" to handle external user authentication via LDAP

[Hans-Rudolf Hotz]

Dear all


Our production server uses Apache to handle external user authentication.

I have now set up a new test server (16.04) which handles external user 
authentication via LDAP using the auth_conf file. This works nicely when 
using an empty database (I have managed to solve all last weeks problems).



I have now connected my test server to a copy of the PostgreSQL database 
used on our production server. I try to log in, and I get:


"This account was created for use with an external authentication 
method, contact...)


and the login fails.


If I now set external = 'f'  in the galaxy_user table, it works


Since manually modifying the database is a bad thing, I just want to 
double check, whether this is the right way to do it?



If so, I will add a line or two to the wiki


Many thanks for your help
Hans-Rudolf



--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

[Hans-Rudolf Hotz]

Hi Dannon

Thank you very much for the quick reply:

Our sysadmin installed:

openldap-devel
cyrus-sasl-devel

on our (Red Hat 7.2) box.

And, I can now run

> . .venv/bin/activate
> pip install python-ldap


looks like it is working nowexcept, that I now have to figure out 
the correct settings in auth_conf.xml




Regards, Hans-Rudolf



On 07/22/2016 01:24 PM, Dannon Baker wrote:

There's an open PR with a few build issues to build a Galaxy-side wheel
for python-ldap here:
https://github.com/galaxyproject/starforge/pull/97, and once that's
resolved it should be automatically installed as a conditional
dependency the usual Galaxy way.

Until then, yeah, a workaround is to activate the virtualenv and pip
install it.  As you found out, to do that you'll need a few system
packages -- I had to install both libldap2-dev and libsasl2-dev on an
ubuntu box here to get it to build.  Good luck!

-Dannon

On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Dear all

I am looking into authentication through LDAP using the auth_conf file
(we are currently using Apache to handle this). And it looks like, I am
stuck at a very early step:


I have started with a fresh checkout of release 16.04
(git clone -b master https://github.com/galaxyproject/galaxy.git)

some modifications in galaxy.ini (host, port) and:

auth_config_file = config/auth_conf.xml


I start galaxy, and I try to login. In the log file I get:

galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
authenticate: email is hansrudolf.h...@fmi.ch
<mailto:hansrudolf.h...@fmi.ch>
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
authenticate: 

This is what I expect...so far so good

but further down, I get:

galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP
authenticate: could not load ldap module


According to our sysadmin, "python-ldap" is installed on the machine
(running Red Hat 7.2). But I assume, it has to be within the galaxy
created virtual env, hasn't-it?


Hence I have tried the following


cd 
. .venv/bin/activate
pip install python-ldap


Is this the right way to do it?


Doing this, I have been running into the following error:

Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
#include "lber.h"


So I guess I have to tell my sysadmin to install "openldap-devel in
order to have 'lber.h' on the system?


Or do I have to do something else?




Thank you very much for your help
Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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[galaxy-dev] activate authentication through LDAP using the auth_conf file

[Hans-Rudolf Hotz]

Dear all

I am looking into authentication through LDAP using the auth_conf file 
(we are currently using Apache to handle this). And it looks like, I am 
stuck at a very early step:



I have started with a fresh checkout of release 16.04
(git clone -b master https://github.com/galaxyproject/galaxy.git)

some modifications in galaxy.ini (host, port) and:

auth_config_file = config/auth_conf.xml


I start galaxy, and I try to login. In the log file I get:

galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741 
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP 
authenticate: email is hansrudolf.h...@fmi.ch
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP 
authenticate: 


This is what I expect...so far so good

but further down, I get:

galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP 
authenticate: could not load ldap module



According to our sysadmin, "python-ldap" is installed on the machine 
(running Red Hat 7.2). But I assume, it has to be within the galaxy 
created virtual env, hasn't-it?



Hence I have tried the following


cd 
. .venv/bin/activate
pip install python-ldap


Is this the right way to do it?


Doing this, I have been running into the following error:

Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
#include "lber.h"


So I guess I have to tell my sysadmin to install "openldap-devel in 
order to have 'lber.h' on the system?



Or do I have to do something else?




Thank you very much for your help
Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] default number of concurrent jobs

[Hans-Rudolf Hotz]

copy job_conf.xml.sample_basic to job_conf.xml and make the changes

(and restart galaxy)

Hans-Rudolf


On 07/15/2016 10:32 AM, Ulf Schaefer wrote:

Hi Hans-Rudolf

That was the first thing that came to my mind as well.

But by default you don't seem to get a "job_conf.xml". You just get
"job_conf.xml.sample_advanced" and "job_conf.xml.sample_basic", so I
assume it is not really using any of those two. However in the
"job_conf.xml.sample_basic" there is a comment saying "". But the number of
workers in there is set to 4. So why 5?

Any ideas?

Thanks
Ulf

On 15/07/16 08:03, Hans-Rudolf Hotz wrote:

Hi Ulf


Have a look at the "job_conf.xml" file, see also:

https://wiki.galaxyproject.org/Admin/Config/Jobs


Regards, Hans-Rudolf



On 07/14/2016 01:35 PM, Ulf Schaefer wrote:

Hi all

I installed an out-of-the-box Galaxy instance on my local machine as per
the instructions (https://wiki.galaxyproject.org/Admin/GetGalaxy). I
have made minimal adjustments beyond making myself an admin.

When I run a workflow in batch mode on 10 data sets it appears to
running 5 concurrent jobs. Why? Does anyone know where that is
configured? Is it dynamically determined based on the number of cores I
have (n=4)?

Thanks for any advice
Ulf

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**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
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Re: [galaxy-dev] default number of concurrent jobs

[Hans-Rudolf Hotz]

Hi Ulf


Have a look at the "job_conf.xml" file, see also:

https://wiki.galaxyproject.org/Admin/Config/Jobs


Regards, Hans-Rudolf



On 07/14/2016 01:35 PM, Ulf Schaefer wrote:

Hi all

I installed an out-of-the-box Galaxy instance on my local machine as per
the instructions (https://wiki.galaxyproject.org/Admin/GetGalaxy). I
have made minimal adjustments beyond making myself an admin.

When I run a workflow in batch mode on 10 data sets it appears to
running 5 concurrent jobs. Why? Does anyone know where that is
configured? Is it dynamically determined based on the number of cores I
have (n=4)?

Thanks for any advice
Ulf

**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
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[galaxy-dev] Swiss German Galaxy Tour/Day 2016 - Freiburg (Germany), 20/21 October

[Hans-Rudolf Hotz]

Dear all


After the big success of the “Swiss German Galaxy Tour” in 2014, we
are going to organize a similar event again in October this year. This
time we meet for two days in Freiburg (Germany):

https://wiki.galaxyproject.org/Events/SG2016

It is our great pleasure to announce that Dannon Baker, a core
developer of the Galaxy team from Johns Hopkins will join us again on
both days.

Like last time, the aim is to discuss the status of the Galaxy
project, new developments, interface to other systems, extensions and
best practice in reproducible research. We also welcome participants
who are using other workflow management systems and tool developers
who are looking for such systems to offer their tools to a wider
audience.


The program is as follows:

Thursday, October 20th: 3rd Swiss Galaxy Workshop.
we intend to have a full day of talks from you. We encourage you
to design your talk problem-centric and use the experience of other
participants to solve them. please provide a preliminary title for a
20-minutes talk or a short presentation, when you register.

Friday, October 21st: 2nd German Galaxy Developer Workshop
this day is more on the technical side, with presentation and
hands on exercises. please provide suggestion for topics to be covered
during this day, when you register.


Registration is now open (space is limited). We recommend you register
soon to secure your spot on one or both days of the SG2016Tour:

http://tinyurl.com/SG2016-reg




Looking forward to see many of you in Freiburg

Regards, Bjoern and Hans-Rudolf


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Re: [galaxy-dev] Docker for Mac

[Hans-Rudolf Hotz]

> On 29 Jun 2016, at 15:57, Philipp Rathert 
>  wrote:
> 
> Hi Hans-Rudolph,
> This means you use 
> Docker pull bgruening/galaxy-stable:latest to get the image?
>  

yesy

> I just noticed that the “latest” image is 6 weeks old and the other only 9 
> days…
>  
> Anyway, I will try if the problems occur with the old one as well. 
>  
> Did you ever tried to use Docker for mac in a production mode, if yes any 
> idea how to allow acces from other computers in the network?


only used for training and demonstration purposes so far. 
haven’t tried to access it over our network, but don’t see a reason why it 
should not work.

Hans-Rudolf




> Cheers,
>  
> Philipp
>  
> From: Hans-Rudolf Hotz [mailto:hansrudolf.h...@fmi.ch 
> <mailto:hansrudolf.h...@fmi.ch>] 
> Sent: Wednesday, June 29, 2016 3:50 PM
> To: Rathert, Philipp, Dr.  <mailto:philipp.rath...@ibc.uni-stuttgart.de>>
> Cc: galaxy-dev@lists.galaxyproject.org 
> <mailto:galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Docker for Mac
>  
> Hi Philipp
>  
> I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have 
> always used the traditional location for the image to fetch from: 
> https://index.docker.io/u/bgruening/galaxy-stable/ 
> <https://index.docker.io/u/bgruening/galaxy-stable/>   (i.e just following 
> the excellent recipes on https://github.com/bgruening/docker-galaxy-stable 
> <https://github.com/bgruening/docker-galaxy-stable> )
>  
> and just by coincidence:  last night I tried 'quay.io/bgruening/galaxy:16.04' 
> <http://quay.io/bgruening/galaxy:16.04'> and it didn’t work, but I haven’t  
> investigated why….
>  
> Hans-Rudolf
>  
>  
>> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>> > <mailto:philipp.rath...@ibc.uni-stuttgart.de>> wrote:
>>  
>> Dear all I was wondering if anybody has experience running a galaxy 
>> production server using docker for mac. I know it's beta testing at the 
>> moment but since the Virtual machine environment gave us such a hard time 
>> preserving and managing user data etc. I thought I try it anyway...
>> 
>> 
>> However, it seems to be not as easy as expected.
>>  
>> after installation of docker I pull the new docker galaxy image with
>> docker pull quay.io/bgruening/ <http://quay.io/bgruening/>galaxy:16.04 
>> 
>> 
>> 
>> When I start a test container with net=host
>> docker run -it --net=host quay.io/bgruening/ 
>> <http://quay.io/bgruening/>galaxy:16.04 ) 
>> 
>> 
>> I am not able to connect to the galaxy web app and get this  error:
>> 
>> 
>> 
>> Starting ProFTP
>> proftpd: ERROR (abnormal termination)
>> 
>> 
>> 
>> 
>> and 
>> 
>> 
>> 
>> 
>> 
>> 
>> ==> /home/galaxy/logs/slurmd.log <==
>> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
>> [2016-06-29T08:13:41.440] error: Unable to establish control machine address
>> 
>> 
>> 
>> 
>> 
>> 
>> I then tried to use Kinematik and at least I get the web app running. 
>> However, I didn't find the option to change the network settings to net=host
>> 
>> 
>> 
>> 
>> 
>> 
>> And I have the additional problem that I have to assign ownership rights to 
>> the folders in /export and I get the following error:
>> 
>> 
>> 
>> 
>> chown -R postgres:postgres  /postgresql
>> chown: postgres: illegal group name
>> 
>> 
>> I know these are many issues, but maybe one of you has experience with this 
>> and could provide some help.
>> 
>> 
>> Thanks a lot,
>> 
>> 
>> Philipp
>> 
>> 
>> 
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>> 
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>> <http://galaxyproject.org/search/mailinglists/>
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Re: [galaxy-dev] Docker for Mac

[Hans-Rudolf Hotz]

Hi Philipp

I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always 
used the traditional location for the image to fetch from: 
https://index.docker.io/u/bgruening/galaxy-stable/ 
   (i.e just following the 
excellent recipes on https://github.com/bgruening/docker-galaxy-stable 
 )

and just by coincidence:  last night I tried 'quay.io/bgruening/galaxy:16.04' 
 and it didn’t work, but I haven’t  
investigated why….

Hans-Rudolf


> On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. 
>  wrote:
> 
> Dear all I was wondering if anybody has experience running a galaxy 
> production server using docker for mac. I know it's beta testing at the 
> moment but since the Virtual machine environment gave us such a hard time 
> preserving and managing user data etc. I thought I try it anyway...
> 
> However, it seems to be not as easy as expected.
> 
> after installation of docker I pull the new docker galaxy image with
> docker pull quay.io/bgruening/galaxy:16.04 
> 
> When I start a test container with net=host
> docker run -it --net=host quay.io/bgruening/galaxy:16.04 ) 
> 
> I am not able to connect to the galaxy web app and get this  error:
> 
> 
> Starting ProFTP
> proftpd: ERROR (abnormal termination)
> 
> 
> and 
> 
> 
> 
> ==> /home/galaxy/logs/slurmd.log <==
> [2016-06-29T08:13:41.440] error: Unable to resolve "moby": Unknown host
> [2016-06-29T08:13:41.440] error: Unable to establish control machine address
> 
> 
> 
> I then tried to use Kinematik and at least I get the web app running. 
> However, I didn't find the option to change the network settings to net=host
> 
> 
> 
> And I have the additional problem that I have to assign ownership rights to 
> the folders in /export and I get the following error:
> 
> 
> chown -R postgres:postgres  /postgresql
> chown: postgres: illegal group name
> 
> I know these are many issues, but maybe one of you has experience with this 
> and could provide some help.
> 
> Thanks a lot,
> 
> Philipp
> 
> ___
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[galaxy-dev] will start in 10 minutes - Re: GalaxyAdmins Meetup This Thursday

[Hans-Rudolf Hotz]

conference room link:

https://connect.johnshopkins.edu/gxyadmins201606/


On 06/15/2016 04:43 AM, Dave Clements wrote:

Hello all,

The June online meetup of GalaxyAdmins will be this Thursday
<https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16>.
This month features two talks:

*1. Galaxy in Production at the University of Minnesota
*
**

Minnesota Supercomputing Institute <https://www.msi.umn.edu/>



Galaxy Radio Telescope <https://github.com/galaxyproject/galaxy/pull/2455>

Galaxy has been deployed in several contexts by the Minnesota
Supercomputing Institute (MSI) <https://www.msi.umn.edu/> at the
University of Minnesota - Twin Citites <https://www.umn.edu/>. This
month Evan Bollig <https://www.msi.umn.edu/staff/evan> and JJ Johnson
<https://www.msi.umn.edu/staff/jj> of MSI will discuss several aspects
of this work relevant to the GalaxyAdmins
<https://wiki.galaxyproject.org/GalaxyAdmins> group:

  *

customizations made to Galaxy that enable MSI to leverage it as a
Tier I service <https://www.msi.umn.edu/services> for our users
(e.g., scheduling, quotas, billing, and sharing).

  *

Pulsar <https://github.com/galaxyproject/pulsar> for Galaxy-P
<https://usegalaxyp.org/> tools on Windows.

  *

the CLIA-certified

<http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatoryAssistance/ucm124105.htm>
 pipelines
and how Galaxy is integrated into clinical workflows

*2. Galaxy Radio Telescope*
*
*

The GRT <https://github.com/galaxyproject/galaxy/pull/2455> aims to
collect job run information from Galaxy servers that opt into the
process. Galaxy Admins can sign in to the GRT, register their Galaxy
servers, and get back API keys per-Galaxy instance. Then they set up a
cron job (preferably weekly, but we may explore options here later), and
submit job data to the GRT.

See
https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16
for full details and links.  The conference room link will be posted an
hour before the meetup.

GalaxyAdmins is a discussion group for Galaxy community members that
administer Galaxy installations.

Hope to see you (online) on Thursday,

Dave Clements and Hans-Rudolf Hotz

--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

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Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

[Hans-Rudolf Hotz]

Hi Martin

we are still on "15.10" (minor version "2")

However, I see the same issues on other public galaxy server which are 
already on 16.04



http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text&name=Homo%20sapiens%20genes%20%28GRCh38.p5%29&URL=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1&resultsButton=1



Hans-Rudolf


On 06/08/2016 04:36 PM, Martin Čech wrote:

Hello Hans-Rudolf,

What version of Galaxy are you using? Can you please share a specific
URL you were sent to that returns a 404?

thanks

M.


On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi all

Please allow me to come back to this old problem:

On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to
http://www.ensembl.org/biomart/martview (see also:

https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b54965fb7af612ac
) and it seems to work, i.e stuff is sent to usegalaxy.org
<http://usegalaxy.org>.

If I try to do the same on our local galaxy server, I still run into the
same problem as last November: the requests are not send to Galaxy, but
end up on the ensembl web page, where they cause a "Error 404 - Page not
found".

Is there anything else, I need to change?


Thank you very much for your help
    Hans-Rudolf



On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:
 > Hi
 >
 > As you probably know, the central BioMart server is currently
 > unavailable (see: http://www.biomart.org/notice.html). Hence, the
"Get
 > Data -> BioMart Central server" tool in our local Galaxy installation
 > does not work anymore - well, this is also the case on
usegalaxy.org <http://usegalaxy.org>.
 >
 >
 > We can easily switch the tool to point to a different Mart
server, i.e.:
 >
 > Change: http://www.biomart.org/biomart/martview"; 
 >
 > to: http://www.ebi.ac.uk/uniprot/biomart/martview"; 
 >
 >
 > However, we would like to switch to the ensembl Mart server:
 >
 > http://www.ensembl.org/biomart/martview
 >
 >
 > It looks like the ensembl Mart server is nowadays embedded in the
 > ensembl web site, and the requests are not send to Galaxy, but
end up on
 > the ensembl web page, where they cause a "Error 404 - Page not
found".
 > Unfortunately, I am not that savvy about the inner works of the
ensembl
 > web site anymore ;)
 >
 >
 > Has anyone else looked into this problem and found already a
solution?
 >
 > Thank you very much for any help
 >
 >
 > Hans-Rudolf
 >
 >
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Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

[Hans-Rudolf Hotz]

Hi all

Please allow me to come back to this old problem:

On usegalaxy.org, the tool is now pointing to 
http://www.ensembl.org/biomart/martview (see also: 
https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b54965fb7af612ac 
) and it seems to work, i.e stuff is sent to usegalaxy.org.


If I try to do the same on our local galaxy server, I still run into the 
same problem as last November: the requests are not send to Galaxy, but 
end up on the ensembl web page, where they cause a "Error 404 - Page not 
found".


Is there anything else, I need to change?


Thank you very much for your help
Hans-Rudolf



On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote:

Hi

As you probably know, the central BioMart server is currently
unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get
Data -> BioMart Central server" tool in our local Galaxy installation
does not work anymore - well, this is also the case on usegalaxy.org.


We can easily switch the tool to point to a different Mart server, i.e.:

Change: http://www.biomart.org/biomart/martview"; 

to: http://www.ebi.ac.uk/uniprot/biomart/martview"; 


However, we would like to switch to the ensembl Mart server:

http://www.ensembl.org/biomart/martview


It looks like the ensembl Mart server is nowadays embedded in the
ensembl web site, and the requests are not send to Galaxy, but end up on
the ensembl web page, where they cause a "Error 404 - Page not found".
Unfortunately, I am not that savvy about the inner works of the ensembl
web site anymore ;)


Has anyone else looked into this problem and found already a solution?

Thank you very much for any help


Hans-Rudolf



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Re: [galaxy-dev] Removing stale references from a history

[Hans-Rudolf Hotz]

Hi Scott

Can you explain a little bit more what you mean by "file references that 
are no longer valid in one of his histories"?


What happens when your user tries to delete the affected history item?


Regards, Hans-Rudolf




On 05/16/2016 06:21 PM, Scott Szakonyi wrote:

Hello,

Due to some problems on our servers, one of our users has file
references that are no longer valid in one of his histories. He's
requested that I remove them, but I don't see any particular way to do
so through the interface. Is there any way to achieve this? I've poked
around in the database but don't see any obvious link between the
history and data files.

Thanks in advance,

--
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu 


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Re: [galaxy-dev] [SPAM] RE: GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools!

[Hans-Rudolf Hotz]

https://connect.johnshopkins.edu/gxyadmins201604/

it is also on the wiki



On 04/21/2016 04:47 PM, Christian Brenninkmeijer wrote:

Can someone please post the joining URL.
Thanks
Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Hotz, Hans-Rudolf [hansrudolf.h...@fmi.ch]
Sent: Monday, April 18, 2016 10:06 AM
To: galaxy-dev@lists.galaxyproject.org
Cc: Hans-Rudolf Hotz
Subject: [galaxy-dev] GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile 
Devices; and Tools, Tools, Tools!

Hello all,

The next <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> 
GalaxyAdmins<https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> online 
meetup<https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_04_21> is this 
Thursday, April 21 at 5PM CET (see your local time<http://bit.ly/1RpBa8e> to know when to 
connect):

The featured topics are:


The Galaxy Portal: Accessing Galaxy from Mobile 
Devices<http://bioinformatics.oxfordjournals.org/content/early/2016/02/17/bioinformatics.btw042.full>

Ivar Grytten<http://www.mn.uio.no/ifi/english/people/aca/ivargry/> and Geir Kjetil 
Sandve<http://www.mn.uio.no/ifi/english/people/aca/geirksa/>, University of 
Oslo<http://www.uio.no/>

Tool Development Developments
John Chilton<https://wiki.galaxyproject.org/JohnChilton>, Penn State 
University<http://psu.edu/>

The meetup will use the same Adobe Connect technology used on previous calls. 
The 'Meeting Room Link' will be provided on the wiki page in time. It takes a 
couple of minutes to connect, so you are encouraged to start connecting a few 
minutes early.

See http://bit.ly/gxyadm201604 for full details.

Thanks,

Dave C and Hans-Rudolf

GalaxyAdmins<https://wiki.galaxyproject.org/Community/GalaxyAdmins> is a 
discussion group for Galaxy community members who are responsible for Galaxy 
installations.
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Re: [galaxy-dev] Allow users to see the job queue?

[Hans-Rudolf Hotz]

Hi Ray

Are you running the reports tool?

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

you can inform your user about this page, and then, they can check the 
"All unfinished jobs" page.


This is probably the easiest way - though you need to consider, that all 
users can see each other jobs (i.e the executed command line) on that 
extra web site



Regards, Hans-Rudolf



On 04/15/2016 09:22 AM, Raymond Wan wrote:

Dear all,

I know Galaxy is independent of the underlying queuing system but is
it possible to display the status of the queue to users via the Galaxy
interface?

I understand that the jobs are submitted under the name of the owner
of the Galaxy process.  And that there is a way to fix this [1], but I
think I'm fine with leaving it as-is.  I guess it would be nice if
users can see how long the queue is.

The naive way that I'm thinking about is to have a cronjob that runs
"squeue" (we are using SLURM) periodically.  Its output is cleaned up
by a script and a "static" HTML file is generated for Galaxy to
display.

I don't know if there is a more sensible way that fits within the
framework of Galaxy.  Is this approach acceptable or is there a better
/ easier way that I've completely missed?

Thank you!

Ray

[1] 
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
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Re: [galaxy-dev] Problem with LDAP authentication

[Hans-Rudolf Hotz]

Hi Scott

what happens when you remove all galaxy related cookies or try accessing 
Galaxy from another desktop/laptop?



Regards, Hans-Rudolf

On 04/07/2016 03:29 AM, Scott Szakonyi wrote:

Hi all,

I'm having some difficulties with logging into my production website. I
get the following error message in the logs:

galaxy.web.framework.webapp WARNING 2016-04-06 18:47:41,852 User logged
in as 'userID' externally, but has a cookie as 'use...@vectorbase.org
' invalidating session

This started rather suddenly today after there was a space crisis on our
hard drive, which is the subject of my other recent email to this list.

We are using LDAP for external authentication. The same LDAP server is
being used by my "Pre" server, and logins are working fine. I've
compared both galaxy.ini and httpd.conf and can't find any discrepancies.

If someone has suggestions to offer, I would surely appreciate them.

Thanks!

--
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu 


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Re: [galaxy-dev] Troubleshooting BAM file upload issues

[Hans-Rudolf Hotz]

Hi Amelia

Does this happen with "Auto-detect" or do you pre-set the data type to 
'bam' ?



Regards, Hans-Rudolf


On 03/22/2016 07:28 PM, Amelia Ireland wrote:

I'm setting up a Galaxy instance on a new server and am having some
issues with BAM file uploads. I'm using the BAM files supplied with
JBrowse for testing purposes. I have Galaxy installed on my laptop and
file uploads are working fine, so it's evidently an issue with the
server and/or OS configuration.

Attempting to upload a BAM file returns the message

"The uploaded binary file contains inappropriate content"

and the upload is empty.

The server is running Scientific Linux and uses the Environment Modules
system for dependency management. I can successfully upload bed and
bigwig files, which suggests that samtools is being loaded and
functioning correctly.

If someone can suggest some troubleshooting steps, I would be most grateful.

Thanks!
Amelia

Integrated Microbial Genomics (IMG)
JGI / LBL



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Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

[Hans-Rudolf Hotz]

Hi Carl

It works !
Thank you very much for providing  a fix so fast.


Regards, Hans-Rudolf

On 03/22/2016 02:26 PM, Carl Eberhard wrote:

https://github.com/galaxyproject/galaxy/pull/1972

Thanks for letting us know about this. Let me know if you spot any
problems with that fix.

On Tue, Mar 22, 2016 at 8:32 AM, Carl Eberhard mailto:carlfeberh...@gmail.com>> wrote:

Hey, Hans

Looks like a problem with the way we're loading the color-picker
library Farbtastic. I'll take a look, try to get a fix out, and
update here today.

Carl

On Mon, Mar 21, 2016 at 9:01 AM, Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Hi all

Since we upgraded our Galaxy installation from 15.05 to 15.10
(plus the recent security fix, changeset: 17161:3f95c21b1a85),
the "Edit settings" button in Trackster is no longer working.
The window, which normally allows you to select the colors, etc.
doesn't show up anymore.

This happens with different browsers on mac and linux. On the
console I get: "TypeError: a.browser is undefined"

Has anyone else seen this problem? Or is there even already a
fix available?


Thank you very much for your help
    Hans-Rudolf








--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] shed_tool_conf.xml

[Hans-Rudolf Hotz]

On 03/22/2016 12:56 PM, Peter Cock wrote:

I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...



probably a lot of 'manual' work including comparing with the admin page 
'Installed tool shed repositories'.


Also, look at the file "integrated_tool_panel.xml". all tools listed 
there which are not listed in "tool_conf.xml" need an entry in 
shed_tool_conf.xmlas far as I know.



Hans-Rudolf





Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
 wrote:

Dear all,


I think I made a really stupid mistake. I edited the shed_tool_con.xml file
to change the order and section of tools.


Doing this I might have introduced an error I cannot locate. However (now
comes the stupidity), I didn't save the old version of the
shed_tool_conf.xml file...


Is there a way to fix this or do I have to reinstall all tools again?


Thank you for your help.


cheers,


Philipp


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[galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

[Hans-Rudolf Hotz]

Hi all

Since we upgraded our Galaxy installation from 15.05 to 15.10 (plus the 
recent security fix, changeset: 17161:3f95c21b1a85), the "Edit settings" 
button in Trackster is no longer working. The window, which normally 
allows you to select the colors, etc. doesn't show up anymore.


This happens with different browsers on mac and linux. On the console I 
get: "TypeError: a.browser is undefined"


Has anyone else seen this problem? Or is there even already a fix available?


Thank you very much for your help
Hans-Rudolf








--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Load tools without service interruption

[Hans-Rudolf Hotz]

Hi Floreline


It depends on the 'source' of the tool:

If you add the tool via Tool Shed, then there is no need to restart the 
Galaxy server. However, if you add a tool manually (i.e. by adding a 
line to tool_conf.xml) you need to restart the server - at least that is 
my current knowledge.



Hans-Rudolf


On 03/01/2016 11:09 PM, Floreline TOUCHARD wrote:

Hi Galaxy team,

Is there a way to add a tool without service interruption ?
Something like a "sh run.sh --reload" (not "restart") command.
I think I saw this information once, but I can't put my hand on it anymore.

Thanks in advance !
F.T



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Re: [galaxy-dev] Galaxy External Authentication and API access

[Hans-Rudolf Hotz]

Hi Lance

just double checking: Have you implemented this fix:

https://github.com/galaxyproject/galaxy/pull/1003
(https://gist.github.com/8d0412367371127e90ad)

This solved our problem with the 'View all histories' nicely - though we 
still have problems with 'Impersonate a user'



Regards, Hans-Rudolf


On 03/01/2016 11:06 PM, Lance Parsons wrote:

I am currently using Apache and CAS
(https://en.wikipedia.org/wiki/Central_Authentication_Service) to
provide external authentication to Galaxy. I'd like to start using the
API, however, I've not been able to find a way to get that to work.

A while back, someone suggested using the following:


 Satisfy Any
 Allow from all


However, this breaks the history view at least, since the ajax call is
an /api call and no HTTP_REMOTE_USER gets set. Does anyone have any
suggestions? I'd love to get this going with some simple configuration...

I know I could move over to LDAP, but that is not desirable since it's
less secure than CAS.

Another option would be to implement CAS within Galaxy, but that does
seem like a good bit of work, but perhaps someone is already working on
it or at least interested?



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Re: [galaxy-dev] Lost prostgresql database

[Hans-Rudolf Hotz]

Hi

To follow up on Peter's suggestion: It might be worth trying to make 
'Galaxy Data Libraries' for all the old individual datasets in your new 
Galaxy installation. This way, you will have sort of easy access to the 
old datasets in you new set-up.


Since the datasets are in distinct folders (database/files/000, 
database/files/001, database/files/002, etc), you can use the option: 
"Upload files from filesystem paths". It will 'auto-detect' the file 
format for you. Though this will take a very, very long time, since you 
have up to 1000 files per directory (you might wanna split the 
directories into smaller chunks). Also, it won't work with complex 
datatypes.


Hans-Rudolf


On 02/26/2016 10:18 AM, Peter Cock wrote:

Hi Amos,

As Hans-Rudolf said, if you really have lost the database and its
backups, there is not much you can do.

If you have just a few very valuable datasets that have to be
recovered, I would look at the file dates (guided by the automatically
incremented dataset numbers), sizes, and look at the data to check
the contents (everything will be named *.dat as the extension,
other than complex datatypes).

Peter

On Fri, Feb 26, 2016 at 9:12 AM, Hans-Rudolf Hotz  wrote:

Hi Amos

Since the PostgreSQL database stores much more than the links to and
previews of the individual datasets, you need to restore it from your
PostgreSQL backup file.

Hans-Rudolf

On 02/25/2016 08:53 PM, Raphenya, Amogelang wrote:


Hi All,

Our server hard drive failed and we lost the database which was running
galaxy instance.

But we did NOT loose all the data i.e all the files are there under
the*/galaxy-dist *directory.
*
*
Is there a way to reconstruct the database using the data itself.

Please help.

/
/
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140//ext: //22787/
/a:1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e: raphe...@mcmaster.ca <mailto:raphe...@mcmaster.ca> /
/skype:amos_raphenya/




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Re: [galaxy-dev] Lost prostgresql database

[Hans-Rudolf Hotz]

Hi Amos

Since the PostgreSQL database stores much more than the links to and 
previews of the individual datasets, you need to restore it from your 
PostgreSQL backup file.


Hans-Rudolf



On 02/25/2016 08:53 PM, Raphenya, Amogelang wrote:

Hi All,

Our server hard drive failed and we lost the database which was running
galaxy instance.

But we did NOT loose all the data i.e all the files are there under
the*/galaxy-dist *directory.
*
*
Is there a way to reconstruct the database using the data itself.

Please help.

/
/   
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140//ext: //22787/
/a:1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e: raphe...@mcmaster.ca  /
/skype:amos_raphenya/




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Re: [galaxy-dev] cleanup

[Hans-Rudolf Hotz]

Hi Philipp


point 1 : that's as expected - good.

point 2 : looks like a docker specific issue? Maybe Bjoern can jump in?


Hans-Rudolf




On 02/23/2016 12:17 PM, Rathert, Philipp, Dr. wrote:

Dear Hans-Rudolf,

thanks a lot for your help.

I did as you suggested:

1. when I go into the scripts folder I get the error message you guessed:
root@galaxy:/galaxy-central/scripts# python
cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -30 -1
Traceback (most recent call last):
File "cleanup_datasets/cleanup_datasets.py", line 21, in 
  import galaxy.config
ImportError: No module named galaxy.config


2. from the root directory I recieve the following error message:
root@galaxy:/galaxy-central# python
scripts/cleanup_datasets/cleanup_datasets.py
/export/galaxy-central/config/galaxy.ini -d -60 -1
Traceback (most recent call last):
File "scripts/cleanup_datasets/cleanup_datasets.py", line 21, in 
  import galaxy.config
File "/galaxy-central/lib/galaxy/config.py", line 21, in 
  from galaxy.util.dbkeys import GenomeBuilds
File "/galaxy-central/lib/galaxy/util/dbkeys.py", line 7, in 
  from galaxy.util.object_wrapper import sanitize_lists_to_string
File "/galaxy-central/lib/galaxy/util/object_wrapper.py", line 45, in

  from six.moves import UserDict
ImportError: cannot import name UserDict

Any idea what this means? I thought this should be automatically
installed with python...

Cheers,

Philipp

     -Original message-
 *From:* Hans-Rudolf Hotz 
 *Sent:* Monday 22nd February 2016 17:09
 *To:* Rathert, Philipp, Dr. ;
 galaxy-dev@lists.galaxyproject.org
 *Subject:* Re: [galaxy-dev] cleanup

 Hi Philipp

 > Since the new galaxy version, I am unable to perform a cleanup anymore.
 >
 >  From the galaxy root directory I want to start the script
 > cleanup_datasets.py with the following line:
 >
 > $ python cleanup_datasets.py /export/galaxy-central/config/galaxy.ini -d
 > -60 -1
 >
 > I get the error message:
 >
 > Can’t open file ‘cleanup_datasets.py’: no such file or directory.

 Have you tried:

 $ python scripts/cleanup_datasets/cleanup_datasets.py
 /export/galaxy-central/config/galaxy.ini -d -60 -1

 > But when I go into the folder in which the script is located it doesn’t
 > work as well.

 what is the error this time? Is it "ImportError: No module named galaxy"?


 Regards, Hans-Rudolf


 > For your information: we are running the latest docker-galaxy-stable
 > version.
 >
 > I hope somebody has an idea.
 >
 > Cheers,
 >
 > Philipp
 >
 > --
 >
 > Philipp Rathert, PhD
 >
 > Institute of Biochemistry
 >
 > University Stuttgart
 >
 > Pfaffenwaldring 55
 >
 > D-70569 Stuttgart
 >
 > Germany
 >
 > Tel: +49 711 685 64388
 >
 > Fax: +49 711 685 64392
 >
 > philipp.rath...@ibc.uni-stuttgart.de
 > <mailto:philipp.rath...@ibc.uni-stuttgart.de>
 >
 > http://www.ibc.uni-stuttgart.de/
 >
 > http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en
 >
 >
 >
 > ___
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 > in your mail client.  To manage your subscriptions to this
 > and other Galaxy lists, please use the interface at:
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 >
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 >http://galaxyproject.org/search/mailinglists/
 >



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Re: [galaxy-dev] cleanup

[Hans-Rudolf Hotz]

Hi Philipp



Since the new galaxy version, I am unable to perform a cleanup anymore.

 From the galaxy root directory I want to start the script
cleanup_datasets.py with the following line:

$ python cleanup_datasets.py /export/galaxy-central/config/galaxy.ini -d
-60 -1

I get the error message:

Can’t open file ‘cleanup_datasets.py’: no such file or directory.



Have you tried:

$ python scripts/cleanup_datasets/cleanup_datasets.py 
/export/galaxy-central/config/galaxy.ini -d -60 -1




But when I go into the folder in which the script is located it doesn’t
work as well.


what is the error this time? Is it "ImportError: No module named galaxy"?



Regards, Hans-Rudolf




For your information: we are running the latest docker-galaxy-stable
version.

I hope somebody has an idea.

Cheers,

Philipp

--

Philipp Rathert, PhD

Institute of Biochemistry

University Stuttgart

Pfaffenwaldring 55

D-70569 Stuttgart

Germany

Tel: +49 711 685 64388

Fax: +49 711 685 64392

philipp.rath...@ibc.uni-stuttgart.de


http://www.ibc.uni-stuttgart.de/

http://www.ibc.uni-stuttgart.de/mitarbeiter/Rathert/?__locale=en



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Re: [galaxy-dev] 18 February GalaxyAdmins Meetup: Ansible, Python Wheels

[Hans-Rudolf Hotz]

quick reminder: the meetup will start in ~30 minutes

the link is:
https://connect.johnshopkins.edu/galaxyadmins201602


Hans-Rudolf

On 02/11/2016 02:03 PM, Hans-Rudolf Hotz wrote:

Hello all,

The next GalaxyAdmins online meetup is next week, on Thursday, February
18 at 5PM CET (see your local time to know when to connect:
http://bit.ly/1nDGAkZ)

https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_02_18


The featured topics are:

  - Automating Galaxy deployment @ artbio.fr: the pros and cons of
Ansible, presented by Marius van den Beek

  - The Wheels on the Galaxy go round and round: Python Wheels in
Galaxy, presented by Nate Coraor


The meetup will use the same Adobe Connect technology used on previous
calls. The 'Meeting Room Link' will be provided on the wiki page in
time. It takes a couple of minutes to connect, so you are encouraged to
start connecting a few minutes early.


Looking forward to our first gathering in 2016

Dave C and Hans-Rudolf






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Re: [galaxy-dev] Bypassing Data Managers?

[Hans-Rudolf Hotz]

Hi Ray

Well, I guess, you can call me 'old-fashioned'  ;)

we still solely rely on manually editing the '*loc' files. The main 
reason we do that: Most of our reference data is first prepared (by 
others) for people using it on the command line, and only in a second 
step we make it available via Galaxy.


Hans-Rudolf


On 02/18/2016 09:00 AM, Raymond Wan wrote:

Hi Hans-Rudolf,

Thank you for getting back to me!

I did take a peak at those files and they seem self-explanatory.  I
think I can do that.  However, I was worried about the message at the
top of:

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

It seemed the method written on that page has now been superseded by
Data Managers?  I was worried editing *.loc files directly with an
editor would break a database and cause more headaches for me.  Is
that not the case or perhaps I can get away with doing it just for the
FASTA files but should still use Data Managers for index generation?

Thank you!

Ray


On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz  wrote:

Hi Ray

If you already have the reference data (as you have written in your first
e-mail), then I suggest you manually add those files (file paths) to

~/tool-data/bowtie2_indices.loc
~/tool-data/bowtie_indices.loc

This way you prevent duplication of your reference data


Regards, Hans-Rudolf




Dear all,

I have gotten a bit further and was able to install the Data Managers
this time.  Previously, I was having problems accessing the ToolShed
web site and some Python errors in the log file, but fine ... sort of
(I get some intermittent errors accessing the Tool Shed site; maybe
it's a problem on my side).

However, with the FASTA fetch tool installed from the Galaxy Main Tool
Shed, I selected "Local Data" from the Administrator panel.  Under
"Run Data Manager Tools", I now have "Bowtie index", "Reference
Genome", etc.  When I click on any of the options under "Run Data
Manager Tools", though, I get a blank page.  I mean, I get a
user-level menu on the left, history on the right, a menu along the
top.  But the center is blank.  Is there something else I need to do?

If I go to "View Data Manager Jobs", "Reference Genome", though, I get
a message that says there are "There are no jobs for this data
manager.".

If possible, I would like to upload FASTA files myself to our local
Galaxy instance.  For reasons which I'm still working on (and which is
unrelated to Galaxy), download times are very long.  Since I have the
FASTA file already, it might be easier to upload one myself; but if
that's not something Data Managers can do, I guess I can just start
the download and set it aside...

Thank you!

Ray



On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan  wrote:


Dear all,

I'm a bit new at being a Galaxy administrator, so apologies for the
basic question.

I need to install some bowtie and bowtie2 indices.  I have the indices
already but came across this page:

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

which says the steps mentioned on that page have been replaced with
Data Managers.  I'm having problems with installing Data Managers
(accessing ToolShed right now and some errors which I guess I need to
sort out later) and was wondering if there was a way to bypass Data
Managers?

Are Data Managers the only way of installing reference data?  With the
indices already pre-calculated, can I install them without having to
go through re-calculating them within Galaxy?

Thank you!

Ray


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Re: [galaxy-dev] Bypassing Data Managers?

[Hans-Rudolf Hotz]

Hi Ray

If you already have the reference data (as you have written in your 
first e-mail), then I suggest you manually add those files (file paths) 
to


~/tool-data/bowtie2_indices.loc
~/tool-data/bowtie_indices.loc

This way you prevent duplication of your reference data


Regards, Hans-Rudolf




Dear all,

I have gotten a bit further and was able to install the Data Managers
this time.  Previously, I was having problems accessing the ToolShed
web site and some Python errors in the log file, but fine ... sort of
(I get some intermittent errors accessing the Tool Shed site; maybe
it's a problem on my side).

However, with the FASTA fetch tool installed from the Galaxy Main Tool
Shed, I selected "Local Data" from the Administrator panel.  Under
"Run Data Manager Tools", I now have "Bowtie index", "Reference
Genome", etc.  When I click on any of the options under "Run Data
Manager Tools", though, I get a blank page.  I mean, I get a
user-level menu on the left, history on the right, a menu along the
top.  But the center is blank.  Is there something else I need to do?

If I go to "View Data Manager Jobs", "Reference Genome", though, I get
a message that says there are "There are no jobs for this data
manager.".

If possible, I would like to upload FASTA files myself to our local
Galaxy instance.  For reasons which I'm still working on (and which is
unrelated to Galaxy), download times are very long.  Since I have the
FASTA file already, it might be easier to upload one myself; but if
that's not something Data Managers can do, I guess I can just start
the download and set it aside...

Thank you!

Ray



On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan  wrote:

Dear all,

I'm a bit new at being a Galaxy administrator, so apologies for the
basic question.

I need to install some bowtie and bowtie2 indices.  I have the indices
already but came across this page:

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

which says the steps mentioned on that page have been replaced with
Data Managers.  I'm having problems with installing Data Managers
(accessing ToolShed right now and some errors which I guess I need to
sort out later) and was wondering if there was a way to bypass Data
Managers?

Are Data Managers the only way of installing reference data?  With the
indices already pre-calculated, can I install them without having to
go through re-calculating them within Galaxy?

Thank you!

Ray

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Re: [galaxy-dev] RedHat versus CentOs

[Hans-Rudolf Hotz]

Dear All

As promised here is the summary of the 9 replies I have received:


CentOS 6  : 6
CentOS 7  : 1

Scientific Linux 6: 2


Regards, Hans-Rudolf


On 01/20/2016 02:20 PM, Hans-Rudolf Hotz wrote:

Dear All

Our production Galaxy server has been running smoothly on a single
multicore box with Red Hat 6.7. As this box gets older and older, it is
in now time to replace it.

At the same time, we are also considering switching the operating system
to CentOS 7. Has anyone switched a production installation from Red Hat
to CentOS ?

'Galaxy Main' is running on CentOS, isn't-it?

I am also interested in plain numbers: how many of you are using Red
Hat, how many CentOS and which version for your production server. I
will probably need such numbers to convince our IT department.

There is no need to reply to the mailing list, just reply to me
(h...@fmi.ch) and if I get enough I will then collate and anonymize all
the data and post back. Maybe we can even add such information to the
wiki (https://wiki.galaxyproject.org/Community/Deployments)?


Thank you very much for your help
Hans-Rudolf



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Re: [galaxy-dev] Filtering dynamic options in tool with tagset

[Hans-Rudolf Hotz]

On 01/27/2016 10:29 AM, Matthias De Smet wrote:

Hi Hans-Rudolf

Thanks again, you’re a lifesaver!
Any suggestions on how I could eliminate the  tag, as the wiki states 
it’s deprecated?


well, it has been 'deprecated' for many years now.



I checked out  but don’t see a straightforward wau to get the same 
results.


same for me  :(


Hans-Rudolf






Matthias


Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz  het volgende 
geschreven:

Hi Matthias

I don't think you can do that...I would delegate the filtering to the 
'list_files' function, i.e. by calling:

list_files(archive_source,query)


Regards, Hans-Rudolf


On 01/27/2016 10:07 AM, Matthias De Smet wrote:


Hi All,

I’m trying to implement a tool that get a list of options through the 
“dynamic_options” tag. I try to filter the options that get returned with 
another param, but it doensn’t seem to work.

my tool xml looks like this


   from the archive to a data library
   
   
 test.sh > $log
   
   
 
   
 
 
   
 
 
 
   
 

   
 
  
   
 
 
   
   
   



Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)

Thanks!
Matthias
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Re: [galaxy-dev] Filtering dynamic options in tool with tagset

[Hans-Rudolf Hotz]

Hi Matthias

I don't think you can do that...I would delegate the filtering to the 
'list_files' function, i.e. by calling:


list_files(archive_source,query)


Regards, Hans-Rudolf


On 01/27/2016 10:07 AM, Matthias De Smet wrote:


Hi All,

I’m trying to implement a tool that get a list of options through the 
“dynamic_options” tag. I try to filter the options that get returned with 
another param, but it doensn’t seem to work.

my tool xml looks like this


   from the archive to a data library
   
   
 test.sh > $log
   
   
 
   
 
 
   
 
 
 
   
 

   
 
  
   
 
 
   
   
   



Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)

Thanks!
Matthias
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Re: [galaxy-dev] Python ValueError: too many values to unpack

[Hans-Rudolf Hotz]

Hi Matthias


Make sure 'listing' is a list of (displayName,value,boolean)

Though, there might be other errors as well


Regards, Hans-Rudolf

I am not sure, whether this
On 01/26/2016 01:22 PM, Matthias De Smet wrote:

Hi all,

I’m trying to develop a tool that lets you select a file on the server.
I’m using the dynamic_options setting to let Galaxy render a dropdown
list of available file.


However, when I try to test the tool in its current form, I get the
following error:


galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught
exception in exposed API method:
Traceback (most recent call last):
   File "lib/galaxy/web/framework/decorators.py", line 260, in decorator
 rval = func( self, trans, *args, **kwargs)
   File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build
 return tool.to_json(trans, kwd.get('inputs', kwd))
   File "lib/galaxy/tools/__init__.py", line 2602, in to_json
 populate_state(trans, self.inputs, state_inputs, state_errors,
params.__dict__)
   File "lib/galaxy/tools/__init__.py", line 2471, in populate_state
 state[input.name] = input.get_initial_value(trans, context,
history=history)
   File "lib/galaxy/tools/parameters/basic.py", line 984, in
get_initial_value
 value = [ optval for _, optval, selected in options if selected ]
ValueError: too many values to unpack


My tool xml looks like this:




   from the archive to a data library
   
   
 test.sh > $log
   
   
 
   
 
 
   
 
 
 

   
 
  
   
 
 
   
   
This tool copies data from and archive folder to your history. Keep in
mind this folder MUST be readable by Galaxy in order for this tool to work.
   




and the script called in the “code” tag looks like this


def list_files(dir,query): listing=[]
for fname in listdir(dir):
  fullpath = path.join(dir, fname) #only select datafiles, not md5
checksums
  if path.isfile(fullpath) and not fullpath.endswith(".md5"):
  listing.append( fname )
return listing


This script should return a list with filenames that should be displayed
in the dropdown list.

I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server

Thanks for your help!

Matthias






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[galaxy-dev] RedHat versus CentOs

[Hans-Rudolf Hotz]

Dear All

Our production Galaxy server has been running smoothly on a single 
multicore box with Red Hat 6.7. As this box gets older and older, it is 
in now time to replace it.


At the same time, we are also considering switching the operating system 
to CentOS 7. Has anyone switched a production installation from Red Hat 
to CentOS ?


'Galaxy Main' is running on CentOS, isn't-it?

I am also interested in plain numbers: how many of you are using Red 
Hat, how many CentOS and which version for your production server. I 
will probably need such numbers to convince our IT department.


There is no need to reply to the mailing list, just reply to me 
(h...@fmi.ch) and if I get enough I will then collate and anonymize all 
the data and post back. Maybe we can even add such information to the 
wiki (https://wiki.galaxyproject.org/Community/Deployments)?



Thank you very much for your help
Hans-Rudolf


--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] tool development

[Hans-Rudolf Hotz]

Hi Matthias

Have you considered "Data Libraries"?

A cron job can query your LIMS and use the API to create "Data 
Libraries". Then the user can select which datasets she/he wants to import.



And back to your original question: Yes, it is possible to create 
interactive tools. Check out the 'dynamic_options' examples on


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


Regards, Hans-Rudolf

On 01/19/2016 12:18 PM, Matthias De Smet wrote:

Hi All,

I would like to create a tool to import data from a sequencer on a networked 
share to a users history.
The ideal setup would be that a query can be submitted to a database which 
contains all metadata from the sequencer + the path of the sequencer output. 
The tool should then show the available datasets found in the database and 
provide checkboxes to select which data should be imported.

My question is: how do you guys propose I get started on this? Do I use the 
API? Is it even possible to get a tool to return some output without submitting 
it as a job, e.g. using it interactively?

Thanks for the help!

PS: I know the basics of tool development, but I haven’t got much experience, 
so all comments are welcome!

Matthias
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Re: [galaxy-dev] Happy new year!

[Hans-Rudolf Hotz]

...and also very special greetings to all Galaxy Admins!

All the Best for the New Year
Hans-Rudolf


PS: the next Galaxy Admin Web Meetup will on Thursday February 18th.
Please let me know, if you want to present your local Galaxy
installation - how you solved or not-solved any specific problems -
at one of the upcoming Meetups. The full schedule is here:
https://wiki.galaxyproject.org/Community/GalaxyAdmins


On 01/01/2016 04:48 AM, Björn Grüning wrote:

Hi Galaxy Developers,

last year was a blast for Galaxy and it seems that the Galaxy core team
is preparing a new release soon with some big big features :)

I really enjoy working with the Galaxy community and wish you all a
happy new year. Let's keep rocking the Galaxy and make Bioinformatics
even more accessible to everyone in 2016.

Happy new year!
Bjoern
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[galaxy-dev] Galaxy job scheduler slows down, when too many jobs are in the queue

[Hans-Rudolf Hotz]

Hi

Over the last few days, I have encountered a very bizarre behavior of 
the internal Galaxy job scheduler. It all started with using the API to 
generate Data Libraries:


Instead of generating individual Data Libraries when requested, I 
decided to make all HiSEQ and MiSEQ data which has been produced in our 
institute for the last two years available.


I used the following call from BioBlend

upload_from_galaxy_filesystem(library_id, filesystem_paths,
folder[0]["id"], type, dbkey='?', link_data_only='link_to_files', roles='')

to link ~19000 (fastq and metadata) files into several sub-folders of 
either the 'HiSEQ' or the 'MiSEQ' Data Library. That all worked very 
well - btw a big Thank You to all the BioBlend developers!


Using the "Data libraries Beta" page I could nicely follow how my script 
is working down all the files.


Unfortunately, I realized too late, that although, the files were 
showing up correctly (i.e with the right path to the original file) in 
the "Data libraries Beta" page, the actual 'upload' job had not been 
finished. So, when my script was done, I ended up with about ~16000 
unfinished jobs waiting in the queue.



We use the internal scheduler, and the settings in the job_conf.xml, 
were set to 2 . At 
the beginning, the  'upload' jobs were running one after the other. 
However, the more jobs were in the queue, the longer it took between the 
two jobs were started. At the hight, two jobs were started only every 
~60 minutes.


During that hour, nothing happened and no job was set to "running". Even 
if someone else was using the Galaxy server, there was a wait of an hour 
for that job to be executed. Luckily I did all this on our development 
server, so no actual user was affected.


I changed the settings in the job_conf.xml file to allow 100 jobs per 
user with a total of 105  concurrent jobs. I restarted the server, and 
now, every hour 100 'upload' jobs were executed. But again, there were 
about 60 minutes in between, when nothing happened.


I was playing with the 'cache_user_job_count' setting ("True"/"False") 
but that didn't change anything.


With 100 jobs executed every hour, the queue became eventually smaller 
and smaller. At about 5000 jobs to go, the gap reduced to ~30 minutes 
and at about 2000  jobs to go, the waiting time was about 10 minutes and 
eventually it went down to zero again.


Has anyone else seen such a behavior before?


Thank very much for any help or suggestions
Regards, Hans-Rudolf



PS: I now modifying the script, with a call to the database to check
whether all jobs have been done, before making the call to upload
more files to the Data Libraries.




--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] Does anybody know if ts (a task scheduler) is supported under Galaxy.

[Hans-Rudolf Hotz]

Hi Shane,


please allow me to jump in late - since you are looking for a simple 
solution: why not rely just on the built in job scheduler? Have a look 
at ~/config/job_conf.xml.sample_advanced


Even on a single box, you can set up different queues with individual 
restrictions.


Hans-Rudolf



On 11/24/2015 06:48 PM, Eric Rasche wrote:

I'd also recommend HTCondor.
Very easy to set up on debian/ubuntu, apt-get has a quick questionnaire that 
gets you up and running.

Cheers,
Eric

On 11/24/2015 11:46 AM, Björn Grüning wrote:

Hi Shane,

would Slurm work for you?

http://slurm.schedmd.com/

Cheers,
Bjoern

Am 24.11.2015 um 13:12 schrieb Shane Kelly:

Hi,
 I am looking for a simple task scheduler to use with Galaxy and
initially picked Torque, but since my server is a single box, Torque
would appear to be overkill?

 Can I have any input from anyone who may have used it?

Thanks for any response
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Re: [galaxy-dev] API key change manually

[Hans-Rudolf Hotz]

Hi Mic

You said, you had migrated your "Galaxy installation to Postgresql"?

So why did you lose your API key? - I assume by 'loosing' you mean: is 
no longer valid, don't you?


Have you forgot to migrate the "api_keys" table? All the keys are stored 
there.



Hans-Rudolf

On 11/17/2015 02:10 PM, Gildas Le Corguillé wrote:

Hello,

I don't know your constraints but you can easily generate a new one:
  - User
  - API Keys
  - Generate a new key now

Gildas


Le 17/11/2015 13:11, Mic a écrit :

Hello,
After I migrated Galaxy installation to Postgresql my API key got
lost. I still know it and would like to add it to the database, but I
am not quite sure how to do it.

How is it possible to add an API key to the database.

Thank you in advance.

Mic


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--
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



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