Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

[Dannon Baker]

Hey Eric,

We use sqlalchemy, and the detailed documentation is here:

http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql

That said, the basic format is:  dialect+driver://username:password@host
:port/database

So, you're going to be looking at something like: postgres://
glxe...@wigserv5.cshl.edu:5432/glxeric



On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric epani...@cshl.edu wrote:

 Hi Dannon,

 There have been some developments, and I would like to update my question
 accordingly.

 I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and
 ferried the database contents over.  My question is this:

 What is the appropriate syntax to use for the parameter
 database_connection in universe_wsgi.ini to use a remote database server?
  Specifically:

 Galaxy host: genomics.cshl.edu
 Database host: wigserv5.cshl.edu
 Database name: glxeric
 Database user/role: glxeric
 Database port: 5432 (postgresql default port)
 Database password: not required under the current configuration.

 Can someone please explain how to fill in the database_connection
 parameter appropriately?

 Many thanks,
 Eric

 
 From: galaxy-user-boun...@lists.bx.psu.edu [
 galaxy-user-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [
 epani...@cshl.edu]
 Sent: Thursday, May 22, 2014 1:38 PM
 To: Dannon Baker
 Cc: Galaxy ‎[galaxy-u...@bx.psu.edu]‎
 Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

 Hi Dannon,

 I have attached a screenshot of the error as it appears in the Galaxy web
 site and a screenshot of the log.

 Please let me know if I can provide any more information.

 Also, please note that the version information I gave for PostgreSQL
 before was incorrect.  I am actually running PostgreSQL 8.1.22.

 Thanks for your assistance,
 Eric

 
 From: galaxy-user-boun...@lists.bx.psu.edu [
 galaxy-user-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [
 epani...@cshl.edu]
 Sent: Thursday, May 22, 2014 11:14 AM
 To: Dannon Baker
 Cc: Galaxy ‎[galaxy-u...@bx.psu.edu]‎
 Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

 Hi Dannon,

 I am in a meeting right now.  I should be done at noon.  I'll send you
 more info then.  Thank you for your assistance!

 Best,
 Eric


  Original message 
 From: Dannon Baker
 Date:2014/05/22 11:08 (GMT-05:00)
 To: Paniagua, Eric
 Cc: Galaxy ‎[galaxy-u...@bx.psu.edu]‎
 Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

 Hey Eric,

 Looking into this.  Can you send the exact error/trace if available?

 -Dannon


 On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric epani...@cshl.edu
 mailto:epani...@cshl.edu wrote:
 Hi,

 I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
 the process of preparing an update I have encountered some problems.  When
 I try to create a new dataset (e.g. by running a tool), I receive an error
 message indicating a syntactic problem with backend database commands.
  Specifically, the error mentions a read-only cursor and occurs when the
 system is trying to look up the history hid number for the new dataset, a
 value which (as far as I understand it) should be an autoincrementing
 primary key.

 My codebase is the 68a8b0397947 commit on the stable branch, plus some
 custom tool definitions, but no real modification to any core Galaxy code.
  The database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In
 the target (production) environment, we run with 3 web server processes and
 3 job runner processes, but I am encountering this error in a
 single-Galaxy-process test instance.  The error is reported both in the
 logs (with a traceback originating in the bowels of SQLAlchemy) and via the
 web interface.

 I dug through the commit history and found a comit (e1bc855165bc) with the
 comment Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL
 9.2.4). on Sep 23, 2013.  I am wondering if this means I need to upgrade
 my database backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that
 I need to keep 2 parallel Galaxy instances running for an extended time
 period (~1 month).  The first is the current (not updated) local Galaxy
 instance, and the second is the new (updated) Galaxy instance, which
 naturally implies diverging databases.  Does this mean I will need to
 maintain parallel installations of PostgreSQL 9.1 and 9.2.x?  How would I
 go about setting up that configuration?

 Any assistance on debugging this error would be greatly appreciated.  Our
 initial goal was to roll out this update tomorrow afternoon, but that may
 need to be delayed because of this show-stopper.  If I can provide any
 further useful information, please let me know, and I will be happy to do
 so.

 Best,
 Eric Paniagua

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Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

[Dannon Baker]

Hey Eric,

Looking into this.  Can you send the exact error/trace if available?

-Dannon


On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric epani...@cshl.edu wrote:

 Hi,

 I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
 the process of preparing an update I have encountered some problems.  When
 I try to create a new dataset (e.g. by running a tool), I receive an error
 message indicating a syntactic problem with backend database commands.
  Specifically, the error mentions a read-only cursor and occurs when the
 system is trying to look up the history hid number for the new dataset, a
 value which (as far as I understand it) should be an autoincrementing
 primary key.

 My codebase is the 68a8b0397947 commit on the stable branch, plus some
 custom tool definitions, but no real modification to any core Galaxy code.
  The database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In
 the target (production) environment, we run with 3 web server processes and
 3 job runner processes, but I am encountering this error in a
 single-Galaxy-process test instance.  The error is reported both in the
 logs (with a traceback originating in the bowels of SQLAlchemy) and via the
 web interface.

 I dug through the commit history and found a comit (e1bc855165bc) with the
 comment Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL
 9.2.4). on Sep 23, 2013.  I am wondering if this means I need to upgrade
 my database backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that
 I need to keep 2 parallel Galaxy instances running for an extended time
 period (~1 month).  The first is the current (not updated) local Galaxy
 instance, and the second is the new (updated) Galaxy instance, which
 naturally implies diverging databases.  Does this mean I will need to
 maintain parallel installations of PostgreSQL 9.1 and 9.2.x?  How would I
 go about setting up that configuration?

 Any assistance on debugging this error would be greatly appreciated.  Our
 initial goal was to roll out this update tomorrow afternoon, but that may
 need to be delayed because of this show-stopper.  If I can provide any
 further useful information, please let me know, and I will be happy to do
 so.

 Best,
 Eric Paniagua

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Re: [galaxy-user] Installing tool in galaxy on cloud

[Dannon Baker]

After adding yourself as an admin in Cloudman, your galaxy instance
restarted, correct?  If so, can you double check that the cloudman admin
interface indicates your exact email address that you've logged into galaxy
as?

-Dannon


On Mon, Feb 3, 2014 at 12:32 PM, Malik, Shivani shivani.ma...@ucsf.eduwrote:

 Hi All,
 I want to use Tophat2 on amazon cloud. I could not find it in the regular
 tools unlike the public server. Am I using the right version?
  I  tried installing it through admin on cloud .Though I was able to make
 myself admin through cloudman instance , I could not see any admin panel on
 Galaxy main page. What am I doing wrong?Any help is appreciated.

 Thanks.
 Shivani

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Re: [galaxy-user] Importing workflow from file fails in Galaxy instance on Amazon Cloud

[Dannon Baker]

Sébastien,

This seems to be a galaxy bug from a little while back.  To fix your cloud
instance, go to the cloud admin console and click Update Galaxy, and the
problem should be resolved once galaxy updates and restarts.

-Dannon


On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau 
sebastien.vign...@gmail.com wrote:

 Hi,

 I can't import workflows from file on a freshly installed instance of
 Galaxy on Amazon Cloud. The error message is copied below. Do you have some
 idea on how to fix this?

 Thanks,

 Sébastien


 Internal Server Error
 Galaxy was unable to sucessfully complete your request
 URL:
 http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow
 Module galaxy.web.framework.middleware.error:149 in __call__
   app_iter = self.application(environ, sr_checker)
 Module paste.recursive:84 in __call__
   return self.application(environ, start_response)
 Module paste.httpexceptions:633 in __call__
   return self.application(environ, start_response)
 Module galaxy.web.framework.base:132 in __call__
   return self.handle_request( environ, start_response )
 Module galaxy.web.framework.base:190 in handle_request
   body = method( trans, **kwargs )
 Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow
   workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
 source=src,add_to_menu=add_to_menu )
 Module galaxy.webapps.galaxy.controllers.workflow:1823 in
 _workflow_from_dict
   module = module_factory.from_dict( trans, step_dict, secure=False )
 Module galaxy.workflow.modules:428 in from_dict
   return self.module_types[type].from_dict( trans, d, **kwargs )
 Module galaxy.workflow.modules:222 in from_dict
   module.state.decode( d[ tool_state ], module.tool,
 module.trans.app, secure=secure )
 Module galaxy.tools:849 in decode
   self.inputs = params_from_strings( tool.inputs, values, app,
 ignore_errors=True )
 Module galaxy.tools.parameters:92 in params_from_strings
   value = json_fix( from_json_string( value ) )
 Module simplejson:384 in loads
 Module simplejson.decoder:402 in decode
 TypeError: expected string or buffer


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Re: [galaxy-user] Grouping Histories into related Projects

[Dannon Baker]

The right approach here is probably to use history tags (at the top of a
history panel, click the tag icon just below the history name).  You could
tag several histories with a particular sample name, organism, etc.  While
you can *search* for histories by tags and get a list of, say, all Mouse
tagged histories, the current Saved Histories grid doesn't display tags in
a particularly useful fashion by default and this could probably be
improved.


On Fri, Nov 1, 2013 at 1:39 PM, Avery DeVries afric...@email.arizona.eduwrote:

 Hello,

 I was wondering if there way any way to group related histories into
 Projects (like a home directory and sub-directories).

 Currently, I have several annotations/analyses in separate histories
 related to the same dataset (i.e. one for gene annotation, one for ENCODE
 elements, etc) and as you can imagine, as I have several other datasets
 each with separate histories for each analysis I conduct, my Saved
 Histories page can get pretty convoluted.

 I would like to keep them in separate histories so I can easily find
 separate analyses, but I really wish there was a way to group them together
 so I could parse through my long list of histories quickly.

 Is this possible to do?  Thank you so much

 Avery

 *Avery DeVries*
 afric...@email.arizona.edu

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Re: [galaxy-user] inconsistant error messages on disk quota?

[Dannon Baker]

Hey Francis,

There's a bug in the current release of cloudman that causes files fetched by 
galaxy (this doesn't affect direct http or ftp upload) to use the root volume 
as temporary storage, which has very little space.  This is fixed in the next 
release scheduled to coincide with the galaxy-dist release.Until that's 
available, I'd recommend using one of the other upload options.  If this isn't 
possible, let me know and I'll try to figure out another workaround.  Sorry for 
the trouble!

-Dannon

On Oct 24, 2013, at 8:45 AM, Francis Ouellette fran...@oicr.on.ca wrote:

 
 I'm on cloudman, trying to upload files, and I'm getting this error message:
 
 No space left on device transferring a 1 GB file to my instance, but the 
 cloudman console says I have more than 5 GB left?
 
 Is this a bad error message?
 
 Is there some other file you want to see?
 
 @bffo
 
 
  
 Screenshot 2013-10-24 13.06.12.png
 
 Screenshot 2013-10-24 13.40.31.png
 
 
 
 -- 
 B.F. Francis Ouellette  http://oicr.on.ca/person/francis-ouellette
 
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Can you send me the more detailed full cloudman log from the admin
interface (it may be quite large).  This will help me see what may have
happened.


On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan leiyan2...@gmail.com wrote:

 Hi all,

 I found some very strange problems on our cloud Galaxy (
 http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.

- It shows galaxy and galaxyIndices have errors in CloudMan Admin
Console.
- This Galaxy had 3 nodes before, but right now only one node is there.
- Galaxy front end still can be opened, but I don’t know it really
works as before or not.

 I attached some screenshot and log files.
 Does anybody have any ideas for this? Thanks a lot.


 Lei Yan
 Center for Integrative and Translational Genomics
 The University of Tennessee Health Science Center

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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Ahh, ok, so you're hitting a bug from a previous release, sorry about that.
 If you're able, updating cloudman itself will fix that (among other small
issues).

That file is also in /mnt/cm as 'paster.log' if you can SSH in to get it.


On Wed, Oct 9, 2013 at 5:18 PM, Lei Yan leiyan2...@gmail.com wrote:

 Dear Dannon,

 When I click the four “Log” links for Galaxy, PostgreSQL, SGE, and Galaxy
 Reports on the Admin Console interface, all of they throw exceptions.
 Please see attachments.
 There is another way I can get the log files?
 Thanks.


 Lei Yan
 Center for Integrative and Translational Genomics
 The University of Tennessee Health Science Center


 On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker dannon.ba...@gmail.comwrote:

 Can you send me the more detailed full cloudman log from the admin
 interface (it may be quite large).  This will help me see what may have
 happened.


 On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan leiyan2...@gmail.com wrote:

 Hi all,

 I found some very strange problems on our cloud Galaxy (
 http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.

- It shows galaxy and galaxyIndices have errors in CloudMan Admin
Console.
- This Galaxy had 3 nodes before, but right now only one node is
there.
- Galaxy front end still can be opened, but I don’t know it really
works as before or not.

 I attached some screenshot and log files.
 Does anybody have any ideas for this? Thanks a lot.


 Lei Yan
 Center for Integrative and Translational Genomics
 The University of Tennessee Health Science Center




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Re: [galaxy-user] How to lauch bulit cluster on Cloudman?

[Dannon Baker]

That means that the galaxy instance for your cluster didn't start.  It
probably should have.  Can you send me (directly, without the list -- it
can contain sensitive info) the cloudman log from the admin panel?

-Dannon


On Tue, Oct 8, 2013 at 9:17 AM, Yan He yanh...@hotmail.com wrote:

 Dear all,

 ** **

 I just established Galaxy Cloudman on Amazon EC2. I created a cluster
 named “exon_capture” and uploaded a lot of data to it. After some analysis,
 I terminated the cluster. The second time I wanted to get access to the
 “exon_capture” cluster, I created a new instance under the “exon_capture”.
 However, under this instance, the “access galaxy” button is in grey and not
 active. I tried several time, but the button was always in grey. Does
 anyone know what’s wrong? Did I miss something? It may be a very simple
 question, but it bothers me a whole afternoon. Thanks a lot!

 ** **

 Yan

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Re: [galaxy-user] galaxy cloud: location of imported and converted fastq's

[Dannon Baker]

Hi PT,

What exactly do you mean by Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were?  Once imported from S3, you're correct in that
everything will be on the local EBS volume.

-Dannon


On Sun, Oct 6, 2013 at 4:43 AM, p Vedell ptved...@hotmail.com wrote:

 Hi,

 ** **

 I had fastq.gz files in an Amazon S3 bucket. I created a Galaxy on the
 Cloud instance using CloudMan. I used GetData and pasted in the url’s of
 the fastq.gz files into Galaxy on the Cloud. They were successfully
 imported into the session and converted to fastq’s, it seems. However, at
 the next step (fastq groomer), Galaxy on the Cloud appears to expect that
 the imported and converted fastq files are in the same S3 bucket where the
 fastq.gz files were. But, they are not there. I read somewhere in
 documentation or notes that the data is actually in /mnt/galaxyData folder.
 However, I am not sure how to point fastq groomer to this place in the web
 interface  or alternatively, I am not sure how to move the fastq’s back to
 the s3 bucket (w/o downloading and re-uploading which would be very
 time-consuming). Thanks for any help you can provide. 

 ** **

 PT

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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Sorry for not being able to take a look at this sooner, thanks for figuring
it out and posting back!  This one must have fallen through the cracks when
we updated all the paths with the last Cloudman release, I'll make a note
to fix it with our next minor update.

-Dannon


On Thu, Sep 26, 2013 at 12:05 PM, Lei Yan leiyan2...@gmail.com wrote:

 Hi all,

 I think I have fixed this bug, and Galaxy GUI can execute MACS
 successfully on my cloud Galaxy.
 I did the following changes to fix it:

- It looks like the latest version of cloud Galaxy uses MACS 1.3, so I
changed the default:

 default - /mnt/galaxy/tools/macs/1.3.7.1/

- There are two path mistakes in the MACS environment variable file
(/mnt/galaxy/tools/macs/1.3.7.1/env.sh), and galaxyTools should be
galaxy:

  PATH=/mnt/galaxy/tools/macs/1.3.7.1/bin:$PATH
  PYTHONPATH=/mnt/galaxy/tools/macs/
 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
  PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH
  PYTHONPATH=/mnt/galaxyTools/tools/macs/
 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH


 Maybe this can help somebody.


 Lei Yan
 Center for Integrative and Translational Genomics
 UTHSC


 On Tue, Sep 24, 2013 at 2:55 PM, Lei Yan leiyan2...@gmail.com wrote:

 Hi all,

 http://galaxyclass.genenetwork.org/
 This cloud Galaxy was built by Cloud Galaxy Launch (
 https://main.g2.bx.psu.edu/cloudlaunch) yesterday.
 I found two problems about MACS on it:

- When I execute MACS on Galaxy GUI, I got a “not found” error.
Please see attachment (error1.png).
- If I login the Galaxy server by ssh, I found it looks like MACS was
already installed on it, please see attachment (error2.png). But if I run
MACS in a terminal, I got another error. Please see attachment 
 (error3.png).

 Anybody has any idea for this? Thanks a lot.


 Lei Yan
 Center for Integrative and Translational Genomics
 UTHSC


 On Tue, Sep 24, 2013 at 2:24 PM, Jennifer Jackson j...@bx.psu.edu wrote:

  Hi Lawrence,

 What version of MACS are you running? The Galaxy wrapper in galaxy-dist
 supports v1.3. I am 99% certain that the latest Cloudman image is the same,
 but Dannon can correct me. The two Tool Shed repos for MACS support v1.4
 and v2.0.10. Making sure that the wrapper  binary are a match might be the
 first place to check - these can get easily confused, especially when
 binaries install with un-versioned symbolic links by default.

 If you are re-running a workflow/job that came from the public Main
 server, and running galaxy-dist/central, then you want to use the v1.3
 binary, unless purposefully upgrading both wrapper  binary. The workflow
 reproducibility tracking will alert you about a change in tool versions and
 permit you to select updated tools upon execution (once tool is configured)
 if from the *same exact wrapper/tool*, but not if a *different
 wrapper/tool/repo* - so will likely take a workflow edit to change out
 the tool in this case if upgrading to newer MACS version.

 I noticed that the tool form README link for the MACS v2.0.10 wrapper is
 incorrect, copy link  add an .rst to find doc. Fairly certain these are
 expected to be .txt - I'll ask our team if this is a Tool Shed or repo
 input issue if extension different.

 Full help for installing tools from the Tool Shed is here:

 http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance

 And current wrapper/binary versions in galaxy-dist/central are listed
 here:
 http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
 With help for managing those dependencies here:
 http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

 Hopefully this helps,

 Jen
 Galaxy team


 On 9/24/13 9:41 AM, Reiter, Larry T wrote:

 Thanks, James. I worked it out by downloading my data files and workflow. 
 For some reason MACS still doesn't work. Any ideas?

 Lawrence T Reiter, PhD
 UTHSC, Memphis, TN


  --
 Jennifer Hillman-Jacksonhttp://galaxyproject.org




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Re: [galaxy-user] Error out of memory when trying to retrieve output

[Dannon Baker]

Do you have debug enabled in your universe_wsgi.ini?  IIRC, this causes the
entire request to be loaded into memory (which is a bad thing when the
response is 20GB).


On Thu, Aug 29, 2013 at 3:50 PM, Delong, Zhou delong.z...@usherbrooke.cawrote:

  Hello,
 I wanted to download the accepted junction .bam file from tophat output of
 my local instance and I get an out of memory error. When I examine the
 server via command line, I found that a python process used by galaxy
 occupied more than 80% of total memory (on the virtual machine with 10G of
 RAM).. I tried curl command to retrieve the datafile after rebooted the
 virtual machine, and python is activated again and used up all the memory.
 The bam is around 20G of size, but I never had this kind of problem with
 other tophat analyses before on my local instance although they are of the
 same size. The discription on the web mentioned some .dat files that I
 manage to find on the disk, but not the bam.
 Can anyone explain what python is doing and how can I solve this please?
 Thanks,
 Delong


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Re: [galaxy-user] cloudman console not responding add/remove nodes

[Dannon Baker]

On Sun, Aug 25, 2013 at 3:35 PM, Deniz Erezyilmaz deniz...@gmail.comwrote:

 When I try to add nodes from the galaxy console, they never register as
 available and the icons never switch from blue to yellow to green. The
 cluster status log shows that they have been added. However, when I try to
 use the remove nodes option, the cluster status log tells me:no idle
 instances found, and I cannot remove the extra instances.


So they remain blue the whole time in the cluster status display?  You
should always be able to terminate extra nodes if you click force removal
of non-idle nodes at terminate, or if you click the node in the cluster
diagram and terminate the specific node from there.  Have you tried this
and found it not to work?

Are you able to share your cloudman log (directly with me is fine -- it can
contain information you wish to keep private)?

The amazon EC2 cloud is showing that the added instances are running, and I
 am being charged for them. I believe the nodes are not actually working
 because the program is running at a snail's pace.


Can you look at the SGE queue (via the cloud admin panel) and see 1) if the
nodes have been registered at all, and 2) if so, what the nodes are doing?
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Re: [galaxy-user] galaxy-user Digest, Vol 86, Issue 17

[Dannon Baker]

Hi Jun,

Thanks for the clarification.  Workflow step annotations would best suit
your needs, I think.  When you're in the editor, click on any step and on
the right side you'll see a field Annotation / Notes which will be
displayed when the workflow is viewed.  This can be used to clear up any
confusion about what the individual step does.

Good luck!

Dannon


On Wed, Aug 21, 2013 at 8:22 PM, Jun Fan j@qmul.ac.uk wrote:

 Hi Jen,

Maybe I have not explained my question cleared which caused the
 confusion: I did not mean the name of dataset.  Actually I asked about the
 display of the tool in the graphic view from the default value (guess it is
 the name attribute in the tool element of the wrapper) to something else in
 the workflow editor. As my ultimate purpose is to share my workflow with
 someone else. If they see three steps with the same displayed name and do
 not have the related knowledge, they will get lost. To help myself to
 explain well, here is the illustration:
 From
 --- ---
 ---
 | mzidLib:PostProcessing|   | mzidLib:PostProcessing|
 | mzidLib:PostProcessing|
 |-| |-|
 |-|
 | input file   |   --| input file
 |
 --| input file|
 |-|   |
 |-|   |
 |-|
 |output (mzid) |-   |output (mzid)
 |-  |output (mzid) |
 --- |-|
 |-|
 To
 -
 ---
 
 | mzidLib:PostProcessing FDR|   | mzidLib:PostProcessing
 Threshold|  | mzidLib:PostProcessing ProteoGroup|
 |--|
 |--|
 |--|
 | input file   |   --| input file
 |   | input file  |
 |--|   |
 |--|   |
 |--|
 |output (mzid) |-   |output (mzid)
 |-  |output (mzid) |
 ---
 |--|
 |--|

 Best regards!
 Jun

 Date: Tue, 20 Aug 2013 11:34:47 -0700
 From: Jennifer Jackson j...@bx.psu.edu
 To: Jun Fan j@qmul.ac.uk
 Cc: galaxy-user@lists.bx.psu.edu
 Subject: Re: [galaxy-user] customize tool display in the workflow
 Message-ID: 5213b6c7.5030...@bx.psu.edu
 Content-Type: text/plain; charset=iso-8859-1; Format=flowed

 Hi Jun,

 You are very close - just click on the create button within the Edit
 Step
 Actions box and it will expand, where you can then enter the new custom
 name. It will look something like this:



 The other post you are referring to is a method to name the output dataset
 based on the input datasets name. You can certainly try this out and see if
 it is useful.

 Hope this helps,

 Jen
 Galaxy team

 On 8/20/13 9:34 AM, Jun Fan wrote:
  Hi  Jennifer,
 
 Many thanks for your reply. Unfortunately I am not clever to
  figure out how to using the existing workflow dataset renaming
  functions. I only know how to rename a dataset within history. Could
  you show me how to do this? I have attached a screen shot of my
  workflow. You can see that I have only managed to add annotation/notes
  to this step. Ideally I would like to have the step with the label of
  mzidLib:PostProcessing FDR  in the graphic view. From other thread,
  someone mentioned to use ${method} in the label, I failed to apply this
 trick.
 
  Best regards!
  Jun
 
  Message: 3
  Date: Mon, 19 Aug 2013 10:18:32 -0700
  From: Jennifer Jackson j...@bx.psu.edu
  To: Jun Fan j@qmul.ac.uk
  Cc: galaxy-user@lists.bx.psu.edu
  Subject: Re: [galaxy-user] customize tool display in the workflow
  Message-ID: 52125368.1060...@bx.psu.edu
  Content-Type: text/plain; charset=iso-8859-1; Format=flowed
 
  Hi Jun,
 
  I asked Dannon (our workflow lead developer) and he suggested just
  using the existing workflow datastet renaming functions. These are in
  the right panel when you click on a dataset within the workflow editor
  (as you probably know).
 
  Inherited naming is not something that is currently being worked on,
  but you can always start a Trello card and see if it gathers votes or
  the attention of a contributor from the larger development community:
  http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board
 
  Take care,
 
  Jen
  

Re: [galaxy-user] problem with custom database build

[Dannon Baker]

Hi Ann,

My guess is that this is related to the issue you were having before.  I'm
taking a look now.

-Dannon


On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S. 
aholtzmor...@chori.org wrote:

 Hi,

 I’m trying to create a new custom build . I keep getting *GURU
 MEDITATION: #aa96a62c69784be49b7864f6ef42ddc6  *I’ve been trying  1 or 2
 times a day for the last 3 days. Thanks

 Ann

 ** **

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[galaxy-user] Fwd: galaxy on the cloud

[Dannon Baker]

Hi Alejandro,

It should show up if you search for the AMI ID, which is ami-da58aab3.
 That said, the easiest way to launch a galaxy cloud cluster if you're not
already familiar with EC2 is probably using usegalaxy.org/cloudlaunch.
 This interface will guide you through the launch process without any extra
input on your part other than providing your AWS keys.
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Re: [galaxy-user] receiving an email when a processing step finishes

[Dannon Baker]

Actually, you can do this in workflows out of the box in Galaxy (as long as
your instance is configured to send mail).

All you need to do is edit the workflow, select the step you want to be
notified following, and add a Step Action- Email Notification.



On Fri, May 17, 2013 at 9:41 AM, Geert Vandeweyer 
geert.vandewey...@ua.ac.be wrote:

  Hi,

 Currently not. For local/cloud instances, you can install an extra tool
 for this from the toolshed:

 http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/sendmail

 best
 geert


 On 05/17/2013 03:01 PM, Nikolay N. wrote:

 Hi,

  I am using the main galaxy instance and have submitted several
 processing steps that seem to have been scheduled for execution. Is there a
 way to get an email notification when such a processing step finishes?

  many thanks,
 Nickyo


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 --

 Geert Vandeweyer, Ph.D.
 Department of Medical Genetics
 University of Antwerp
 Prins Boudewijnlaan 43
 2650 Edegem
 Belgium
 Tel: +32 (0)3 275 97 56
 E-mail: 
 geert.vandewe...@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726


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Re: [galaxy-user] fastq quality trimmer

[Dannon Baker]

Hi Tomaž,

The script depends on galaxy libraries, but could probably be set up
standalone if you made the appropriate libraries available -- the source is
distributed with galaxy, see
https://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default

-Dannon



On Wed, Apr 17, 2013 at 7:30 AM, Tomaz Rijavec to...@ifb.si wrote:

 Dear Galaxy Team,

 I have a question regarding the fastq quality trimmer (by sliding window)
 tool. What is the script running behind it? Is it a modified version of the
 fastx_quality_trimmer found in the fastx tools package? Is there a
 standalone version of it one can set up locally and run it from the command
 line.
 Thanks for all the info you can provide.

 best regards,
 Tomaž





 --
 Lep pozdrav / Best Regards,
 dr. Tomaž Rijavec
 
 Inštitut za fizikalno biologijo d.o.o. / Toplarniška ulica 19, 1000
 Ljubljana / T: 01 587 54 70 / www.ifb.si
 Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana,
 Slovenia / T: +3861 587 54 70 / www.ifb.si

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Re: [galaxy-user] Galaxy on one computer not showing latest runs in history

[Dannon Baker]

Dikla,

After refreshing the browser, the most up-to-date view of the history should 
definitely be available.  Are you positive you're looking at the same history 
in both places?  I would verify that there's nothing in Saved Histories that 
looks like what you're expecting.

-Dannon

On Feb 13, 2013, at 1:43 AM, Dikla Aharonovich dahar...@univ.haifa.ac.il 
wrote:

 Hi
 I am running galaxy and am working both from home and work. 
 Last night at home, my history had up to 35 items in it, that all ran.
 At work today, I can only see 30. This includes number 27 in my history, 
 which shows that it is still running, while I already saw the results for it 
 at home last night.
 I tried logging in and out, and pressing the refresh button.
 Please let me know what else may be causing this
 Many thanks,
 Dikla
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Re: [galaxy-user] gather results from multiple histories

[Dannon Baker]

Hey Mark,

Yep, sure can.  Just click on the gear in the history panel and go to Copy 
Datasets, and copy those datasets you're interested in to th specific new 
history you want to use.

-Dannon

On Feb 1, 2013, at 10:15 AM, mark.r...@syngenta.com wrote:

 Hi All
  
 Let’s say that I have results produced from a step in multiple different 
 histories and that I now want to gather these results into a new history so 
 that they can be joined.  Is there a way to do this without exporting results 
 to my desktop and then uploading?
  
 Thanks
  
 Mark
  
 
 
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Re: [galaxy-user] [galaxy-dev] Workflows

[Dannon Baker]

Geert, this is great stuff!

One small correction -- the API is enabled by default as of revision 
7022:8376ad08ae41 (April 2012).

-Dannon


On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote:

 Hi, 
 
 I've put together some exempels for activating and using the api. You can 
 find them here: 
 
 http://geertvandeweyer.zymichost.com/index.php?page=readid=29
 
 Best regards, 
 
 Geert vandeweyer
 
 Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende 
 geschreven:
 
 Hi
Sorry if these questions are obvious but I just don’t know how to find 
 the answers.
  
 I’m trying to get one of the API examples to work in 
 http://wiki.galaxyproject.org/Learn/API/Examples .
  
 I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e 
 in the examples). I’ve created workflow but don’t know how to access this 
 key.
  
 Also in the first example it states galaxy_url/api/workflows However I 
 don’t have the “api/workflows” directory structure in my galaxy-dist, do I 
 need to create this?
  
 Thanks
 Neil
  
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Re: [galaxy-user] galaxy cloudman login

[Dannon Baker]

To be clear, your admin user still works on this instance but another one does 
not?  If this is the case, can you log in as the admin user (and, if not, 
simply register a new user and make it an admin) and take a look at the user 
list in the admin panel?

To get to the user list when in Galaxy, just click Admin at the top and then 
Manage Users.  Are there users listed?  If your user is listed but you're 
unable to log in, you can reset your password here.

-Dannon


On Dec 31, 2012, at 10:41 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:

 Hello,
  
 I have galaxy cloudman running and had tried one time success to log in to 
 retain the previous data and history after re-launching followed by 1sttime 
 restart. Today I am re-launching again along with the correct size of ebs 
 volumes that I adjusted earlier. However, my login is not recognized at all 
 (“error:no such user….”). I tried several time of terminating and restarting 
 and it is still the same. My admin which is same as the login was able to 
 retained every time. What’s the issue with the log in??
  
 It is taking time to repeat previous data/history. I need your help to 
 retrieve my login.
  
 Thank you in advance,
 Kathryn
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 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
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Re: [galaxy-user] [External] Re: galaxy cloudman login

[Dannon Baker]

On Jan 2, 2013, at 5:17 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
 1. how to retain my previous work?

If you were logged in when you were working previously, we just have to figure 
out who you were logged in as, and log back in.  You may also want to check 
Saved Histories to make sure you aren't unintentionally in a fresh history 
instead of the one you want.

 2. I could not find Mange User under admin, either from cloudman and galaxy 
 web. Where is it?

This is from within the Galaxy interface, not cloudman.  Click Admin in the 
top masthead, and then on the left side you should see a bunch of options.  The 
first of these should be Manage users.

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Re: [galaxy-user] [External] Re: galaxy cluster nodes from the cloudlaunch site

[Dannon Baker]

In the main (non-admin) cloudman UI you'll see a little icon next to the volume 
size.  Click this and you'll have the opportunity to enter a new size.  Upon 
submitting this, galaxy will need to temporarily shut down, but it should be 
automatically restarted once the procedure is complete.  Note that resizing can 
take quite some time (hours, even) depending on the size of the EBS volume in 
question.


On Dec 27, 2012, at 10:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:

 Thanks for the information. Would you help providing further information on 
 expanding ebs volume via cloudman UI? 
 Thank you in advance,
 Kathryn
 
 -Original Message-
 From: dannonba...@me.com [mailto:dannonba...@me.com] 
 Sent: Thursday, December 27, 2012 10:03 AM
 To: Sun, Wenping [USA]
 Cc: galaxy-u...@bx.psu.edu
 Subject: [External] Re: [galaxy-user] galaxy cluster nodes from the 
 cloudlaunch site
 
 
 The root size for the worker nodes doesn't matter.  The only thing relevant 
 to Galaxy here are the available compute units and memory.
 The only storage and working space used is actually attached to the master 
 node (the EBS volume you configure at initial launch) and shared over NFS 
 with the workers.  If you find yourself needing more space, you can expand 
 this volume through the cloudman UI if you want.
 
 
 
 -Dannon
 
 
 
 Sun, Wenping [USA] wrote:
 
 
 
 .sanitized-message p.MsoNormal, .sanitized-message li.MsoNormal, 
 .sanitized-message div.MsoNormal { margin : 0in; margin-bottom :
 .0001pt; font-size : 11.0pt; font-family : Calibri,sans-serif; } 
 .sanitized-message a:link, .sanitized-message span.MsoHyperlink { color : 
 blue; text-decoration : underline; } .sanitized-message a:visited, 
 .sanitized-message span.MsoHyperlinkFollowed { color :
 purple; text-decoration : underline; } .sanitized-message
 span.EmailStyle17 { font-family : Calibri,sans-serif; color :
 windowtext; } .sanitized-message .MsoChpDefault { font-family :
 Calibri,sans-serif; } .sanitized-message div.WordSection1 { }
 
 
 Dear Galaxy users,
 
 I created galaxy instance using galaxy ami the first time. When I re- launch 
 via cloudlaunch site the 2nd time, I have question on adding cluster nodes. 
 There are several pull-down options for the nodes type, no matter which type 
 I choose, they always generate nodes with only 15gb. Is there other option I 
 can have option to define the root space for the nodes?
 
 Thank you,
 Kathryn
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Re: [galaxy-user] galaxy cloudman login and aws instance

[Dannon Baker]

It looks like you've worked on both the public galaxy site we provide 
(main.g2.bx.psu.edu) and your own cloud instance.  Data on the public instance 
won't be automatically migrated to the cloud instance and vice versa.

All work done on the cloud site will remain there and persist after termination 
and restart of that cloud cluster.  Work on main.g2.bx.psu.edu is completely 
separate and will remain there.

-Dannon


On Dec 20, 2012, at 12:44 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:

 Dear galaxy members,
  
 I have question on galaxy running on cloud with the issue of authorization 
 matter.
  
 I have launched aws galaxy cloudman instances to work with, shutting down the 
 cluster afterwards. Then the 2nd time here are the steps that I did—
  
 1.   Launch the galaxy at cloudlaunch site
 2.   Register and then log in
 3.   Worked with data uploading and processing (the login information can 
 see from pull-down menu), as well as the data history
  
 image001.jpg
  
 4.   Go to aws console to check, find the instance is running
 5.   Copy the dns site followed by /cloud to check the cluster nodes, 
 click “access galaxy” button there
 6.   On the galaxy window choose user login
 7.   And here is the window I have – I cannot login and no history data 
 there.
  
 image002.jpg
  
  
 My question:
 it seems that the two galaxy access is not the same. I rather to use the site 
 from cloudlaunch site if it is preferred. However, I still have to go to the 
 instance DNS site for shutting down the instance/cluster to avoid aws 
 unnecessary charge. And, if I need to add cluster nodes, I still need to go 
 to the DNS site.
  
 What is the appropriate procedure I need to follow to retain the data history 
 and log in between two accesses, especially while shutting down and restart?
  
 I really appreciate your inputs and helps!
 Kind regards,
 Kathryn
 ___
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 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
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 please use the interface at:
 
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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

Ahh, ok.  If you want to work exclusively on main and don't have the need for a 
cloud instance, just terminate (and permanently delete, if desired) cloud 
instances through the cloudman interface and keep using main.g2.bx.psu.edu.

-Dannon


On Dec 20, 2012, at 1:41 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:

 Thanks and my question is--
 
 How to shutting down the cloud if working on main.g2.bx.psu.edu?
 
 Thanks,
 Kathryn
 
 -Original Message-
 From: Dannon Baker [mailto:dannonba...@me.com] 
 Sent: Thursday, December 20, 2012 1:38 PM
 To: Sun, Wenping [USA]
 Cc: galaxy-u...@bx.psu.edu
 Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws instance
 
 It looks like you've worked on both the public galaxy site we provide 
 (main.g2.bx.psu.edu) and your own cloud instance.  Data on the public 
 instance won't be automatically migrated to the cloud instance and vice versa.
 
 All work done on the cloud site will remain there and persist after 
 termination and restart of that cloud cluster.  Work on main.g2.bx.psu.edu is 
 completely separate and will remain there.
 
 -Dannon
 
 
 On Dec 20, 2012, at 12:44 PM, Sun, Wenping [USA] sun_wenp...@bah.com 
 wrote:
 
 Dear galaxy members,
 
 I have question on galaxy running on cloud with the issue of authorization 
 matter.
 
 I have launched aws galaxy cloudman instances to work with, shutting 
 down the cluster afterwards. Then the 2nd time here are the steps that 
 I did-
 
 1.   Launch the galaxy at cloudlaunch site
 2.   Register and then log in
 3.   Worked with data uploading and processing (the login information 
 can see from pull-down menu), as well as the data history
 
 image001.jpg
 
 4.   Go to aws console to check, find the instance is running
 5.   Copy the dns site followed by /cloud to check the cluster nodes, 
 click access galaxy button there
 6.   On the galaxy window choose user login
 7.   And here is the window I have - I cannot login and no history data 
 there.
 
 image002.jpg
 
 
 My question:
 it seems that the two galaxy access is not the same. I rather to use the 
 site from cloudlaunch site if it is preferred. However, I still have to go 
 to the instance DNS site for shutting down the instance/cluster to avoid aws 
 unnecessary charge. And, if I need to add cluster nodes, I still need to go 
 to the DNS site.
 
 What is the appropriate procedure I need to follow to retain the data 
 history and log in between two accesses, especially while shutting down and 
 restart?
 
 I really appreciate your inputs and helps!
 Kind regards,
 Kathryn
 ___
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 analysis and other features on the public server at usegalaxy.org.  
 Please keep all replies on the list by using reply all in your mail 
 client.  For discussion of local Galaxy instances and the Galaxy 
 source code, please use the Galaxy Development list:
 
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 http://lists.bx.psu.edu/
 

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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

On Dec 20, 2012, at 2:33 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:

 Thank you very much for the information.
 
 For the last part of using ec2 instances at aws, is there an option that I 
 can control galaxy's operation at aws site? This way I can start/stop the 
 instance when I need. I am not willing to terminate the instance since 
 everything will be lost. 

We'd recommend you not ever stop/start through the aws console -- this is 
basically guaranteed to cause problems with your instance.  Always use the 
cloudman interface (on your ec2 instance -- http://ec2_instance/cloud) to 
terminate, and then use usegalaxy.org/cloudlaunch to restart it.

 Meantime, I am wondering the data structure on ec2 galaxy instance. Where is 
 the location for the data uploaded from the galaxy gui? If I ssh the Ubuntu, 
 where is the data directory for holding the work?

Everything will be in /mnt/galaxyData/files (which is symlinked to 
/mnt/galaxyTools/galaxy-central/database/files).  Note that the filenames will 
be by id (like files/000/dataset_001.dat is dataset id 1, etc), and not 
particularly accessible in this format without a little extra legwork.
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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

On Dec 20, 2012, at 2:52 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
 The problem is that if use usegalaxy.org/cloudlaunch to restart galaxy, it 
 will launch to main.g2.bx.psu.edu, where I have no control on the data 
 security and running queues. Meanwhile, the correspondingly initiated ec2 
 instance is brand new and has no previous work records to track with. 

This isn't quite correct, but I think I see the confusion.

When you launch an instance using usegalaxy.org/cloudlaunch it actually does 
start an instance in the cloud.  A link to your new instance should be 
presented to you on a page saying something like While it may take a few 
moments to boot, you will be able to access the cloud control panel at your 
instance id.  If you don't click on that link to your new instance but 
instead just click Analyze Data in the masthead of that page you're going to 
go back to usegalaxy.org, which is the same server as main.g2.bx.psu.edu.

So, for your use in the cloud you want to launch using 
usegalaxy.org/cloudlaunch, but make sure you're actually *using* the instance 
this starts for you, and *not* galaxyproject.org(main.g2.bx.psu.edu), even 
though we use that server to launch your personal cloud instance.
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Re: [galaxy-user] [External] Re: question on galaxy reference genome window

[Dannon Baker]

On Dec 19, 2012, at 11:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
 I also have the preconfigured cloud instance set up recently. However, when I 
 stopped the instances (master and cluster nodes) from aws, I couldn't get the 
 galaxy web running again (the instance running however the DNS not able to 
 access). What is the right steps to stop the instances and restart it next 
 time?

The cloud deployment isn't designed to be stopped/started through the AWS 
console -- that'll definitely cause problems.  Instead, just terminate the 
instance through the cloudman interface and when you want to use the cluster 
again simply use the same clustername and start a new instance.  The old data 
will be automatically mounted (the cluster details are saved in S3 and the data 
is all on an EBS volume that's persisted in your account) and you'll be right 
back where you left off.
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Re: [galaxy-user] Galaxy server configuration - what is [server:main]?

[Dannon Baker]

That's just the section demarcation stating that everything following (until 
the next such bracketed line) is a property of the 'server:main' section -- 
there should be no need to change that, though you can certainly change any of 
the properties within the section as needed.

-Dannon


On Nov 16, 2012, at 8:59 AM, greg margeem...@gmail.com wrote:

 I see this setting at the top of universe_wsgi.ini:
 
 # Configuration of the internal HTTP server.
 
 [server:main]
 
 I'm confused what that's for.  Do I need to change it?
 
 Thanks,
 
 Greg
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Re: [galaxy-user] tophat

[Dannon Baker]

It isn't normal, but this can happen during periods of extremely high load like 
we're currently experiencing.  If you leave your jobs in the queue, they'll 
execute as soon as possible - don't cancel or restart your jobs as this will 
only move them to the back of the queue and delay completion.

-Dannon

On Nov 8, 2012, at 5:13 AM, Vevis, Christis christis.vevis...@ucl.ac.uk 
wrote:

 Hi all,
  
 I am trying to perform tophat for illumina from the main server of galaxy and 
 is in queue for 24 hours…is that normal??
  
 Regards
  
 Kristis Vevis, PhD Student
 Cell Biology
 UCL Institute of Ophthalmology
 11-43 Bath Street
 London
 EC1V 9EL, UK
 020 7608 4067
  
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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

Lei -

It looks like you have two worker nodes, but both are currently listed as 
non-idle, yet have low load.  My guess is that something has gone wrong with 
the SGE configuration causing jobs to simply wait in the queue.  If you look at 
the contents of qconf and qstat on the admin page, does it look like there are 
jobs backed up and/or worker nodes processing the queue?  Depending on how 
comfortable you are working with SGE, it might be easiest to just click 
restart for SGE in the admin panel and see if everything goes back to normal.

-Dannon


On Nov 8, 2012, at 12:43 PM, Lei Yan leiyan2...@gmail.com wrote:

 Dear Dannon,
 
 My name is Lei Yan, and I am a systems administrator at UTHSC.
 I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most 
 functions work well at that time.
 http://galaxycloud.genenetwork.org/
 But from the day before yesterday, jobs were hung up always. In my opinion, I 
 didn’t find any reasons, because all look correct from Galaxy Admin page (see 
 attachments please).
 Would you please help us to check it? I can give you the administrator 
 password if you need.
 Thanks so much.
 
 
 Lei Yan
 leiyan2...@gmail.com
 UTHSC
 
 
 
 On Wed, Nov 7, 2012 at 4:07 PM, Larry Reiter lrei...@uthsc.edu wrote:
 Dannon,
 
 Maybe you can, but not through me.  I'm just a lowly user and biologist.  You 
 would have to contact the guy who did the installation and runs the server: 
 Lei Yan (leiyan2...@gmail.com)
 
 I would think he would be receptive to some help, so you should mail him.
 
 LTR
 
 On 11/7/12 4:05 PM, Dannon Baker wrote:
 Main will complete the jobs eventually, though obviously that's not 
 particularly useful in the context of your class today.  How is your cloud 
 instance set up?  Cloud or local instances should be the best and most 
 reliable option for teaching with and I'd definitely like to figure out why 
 yours failed.
 
 -Dannon
 
 
 On Nov 7, 2012, at 3:57 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three 
 hours ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 
 lrei...@uthsc.edu
 
  wrote:
 
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there 
 something I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 
 901-448-2635
  (Office)
 
 901-448-7440
  (FAX)
 
 901-448-7443
  (Lab)
 e-mail: 
 
 lrei...@uthsc.edu
 
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at 
 usegalaxy.org
 .  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
  
 
 http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 
 
 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:
 
  
 
 http://lists.bx.psu.edu/
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 
 901-448-2635
  (Office)
 
 901-448-7440
  (FAX)
 
 901-448-7443
  (Lab)
 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 2012-11-07 13-35-01.png2012-11-07 13-36-16.png


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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

NGS jobs are experiencing significant delays at this time due to load -- we're 
looking into it.  Regarding the local install I'd have to recommend pinging the 
administrator on site there -- they should be able to help out.

-Dannon

On Nov 8, 2012, at 10:44 AM, Larry Reiter lrei...@uthsc.edu wrote:

 It looks like both the main server and our local install are frozen.  Nothing 
 has run since we started yesterday at about 11:30am.  Anybody know why?
 
 LTR
 
 On 11/7/12 4:05 PM, Dannon Baker wrote:
 Main will complete the jobs eventually, though obviously that's not 
 particularly useful in the context of your class today.  How is your cloud 
 instance set up?  Cloud or local instances should be the best and most 
 reliable option for teaching with and I'd definitely like to figure out why 
 yours failed.
 
 -Dannon
 
 
 On Nov 7, 2012, at 3:57 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three 
 hours ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 
 lrei...@uthsc.edu
 
  wrote:
 
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there 
 something I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: 
 
 lrei...@uthsc.edu
 
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
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 To manage your subscriptions to this and other Galaxy lists,
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 -- 
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 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
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 901-448-7440 (FAX)
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 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-1160 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
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 Reiter Citation Index

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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

Main will complete the jobs eventually, though obviously that's not 
particularly useful in the context of your class today.  How is your cloud 
instance set up?  Cloud or local instances should be the best and most reliable 
option for teaching with and I'd definitely like to figure out why yours failed.

-Dannon


On Nov 7, 2012, at 3:57 PM, Larry Reiter lrei...@uthsc.edu wrote:

 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three hours 
 ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there something 
 I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
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 at usegalaxy.org.  Please keep all replies on the list by
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 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:
 
  
 http://lists.bx.psu.edu/
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study

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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

They were introduced and described in this news brief (with screenshots!): 
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_05_20

Hope this helps,

Dannon


On Oct 30, 2012, at 7:33 PM, neil.burd...@csiro.au wrote:

 Thanks Bjorn,
 But I can't seem to locate the symbol/icon (looks like papers). 
 Is there any documentation where it is located on the screen?
 
 Thanks
 Neil
 
 -Original Message-
 From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] 
 Sent: Friday, 26 October 2012 9:47 PM
 To: Burdett, Neil (ICT Centre, Herston - RBWH)
 Cc: galaxy-user@lists.bx.psu.edu
 Subject: Re: [galaxy-user] Batch jobs...
 
 Hi Neil,
 
 if you run your workflow, there is small little symbol/icon (looks like 
 papers). If you click these ... you can select multiple input files at once. 
 Also you can probably use the Galaxy API for your task [1].
 
 Happy research!
 Bjoern
 
 [1] http://wiki.g2.bx.psu.edu/Learn/API
 
 Hi,
   I've created a workflow that works well. The workflow accepts 2 input 
 files. After uploading all my input files (there is a lot). How can I batch 
 the process, because I don't want to select files manually and run each job 
 manually. Is there a way to batch this action?
 
 Thanks
 Neil
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 --
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 Albert-Ludwigs-Universität Freiburg
 Institute of Pharmaceutical Sciences
 Pharmaceutical Bioinformatics
 Hermann-Herder-Strasse 9
 D-79104 Freiburg i. Br.
 
 Tel.:  +49 761 203-4872
 Fax.:  +49 761 203-97769
 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
 Web: http://www.pharmaceutical-bioinformatics.org/
 
 Tel.:  +49 761 203-4872
 Fax.:  +49 761 203-97769
 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
 Web: http://www.pharmaceutical-bioinformatics.org/
 
 
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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

Ahh, I see what's going on.  Galaxy relies on the Input Dataset step for this 
feature.  If you use these in your workflow, Galaxy will be able to perform the 
batch execution.  Find them in the workflow editor under Workflow control - 
inputs.

-Dannon


On Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:

 Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I 
 attach screenshots of what I've got (I have a recent subversion checkout)...
  
 Thanks
 Neil
  
  
 image001.jpg
  
  
  
 image002.jpg

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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

Connect the Input Dataset workflow step to the dataset input of the step you'd like to run multiple inputs across, like below. With that example workflow, I can select a batch of inputs that will *all* be mapped with BWA.On Oct 30, 2012, at 9:04 PM, neil.burd...@csiro.au wrote:Thanks Dannon, I can see them now but how do I use them now? As I now have 3 steps:Input File (as before)Input Dataset (new)Atlas list (as before)I select the "Input file" in step 1, and atlases in step 3 (as before) and I can select multiple files for the Input Dataset (but how does that tie into step 1 and 3 as its not connected on the workflow diagram? Neil-Original Message-From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, 31 October 2012 10:54 AMTo: Burdett, Neil (ICT Centre, Herston - RBWH)Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.eduSubject: Re: [galaxy-user] Batch jobs...Ahh, I see what's going on. Galaxy relies on the "Input Dataset" step for this feature. If you use these in your workflow, Galaxy will be able to perform the batch execution. Find them in the workflow editor under "Workflow control" - inputs.-DannonOn Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)...ThanksNeilimage001.jpgimage002.jpg___
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Re: [galaxy-user] Galaxy not showing my reference genome in Drop down for BowTie

[Dannon Baker]

Looking at your screenshot, you have Use a built-in index selected.  If you 
change this to Use one from the history, do you see your fasta file listed?

-Dannon

On Oct 10, 2012, at 9:02 AM, greg margeem...@gmail.com wrote:

 Thanks Jen.  But it looks like the datatype was already set to fasta.
 I tried setting it again and saving but it didn't seem to help.
 
 Is there anything else I can try?
 
 thanks,
 
 Greg
 
 On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson j...@bx.psu.edu wrote:
 Hi Greg,
 
 Nice pic, it helps! My guess is that the datatype is not assigned as
 fasta. To do this, click on the pencil icon for the custom reference
 genome dataset (#1) to bring up the Edit Attributes forms in the center
 panel. Then click on the Datatype tab and change this to be fasta and
 save.
 
 Full help in our wiki with Custom genomes starts here:
 http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
 
 Please let us know if you need more help,
 
 Jen
 Galaxy team
 
 
 
 
 On 10/9/12 11:08 AM, greg wrote:
 
 Hi guys,
 
 As shown in the attached screenshot I uploaded a fasta file.  And I
 want to use it as my reference genome for running bow tie but it
 doesn't appear in the dropdown on the bow tie tool.
 
 I'm sure I'm missing something obvious.
 
 Thanks,
 
 Greg
 
 
 
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Re: [galaxy-user] Cloudman share string not working

[Dannon Baker]

My hunch is that there's a race condition during boot that I haven't had a 
chance to track down and fix yet.  I've actually disabled the share_string 
launch parameter using Galaxy's built-in cloudlaunch until this has been fixed. 
 You can definitely still use the share string, but start the instance without 
specifying it via your launcher (cloudlaunch, biocloudcentral, or manually in 
user data) and enter it in the initial configuration dialog for the instance 
instead.

-Dannon

On Sep 18, 2012, at 9:44 AM, greg margeem...@gmail.com wrote:

 Hi guys,
 
 I entered my share string
 cm-808d863548acae7c2328c39a90f52e29/shared/2012-09-17--19-47 on this
 page https://biocloudcentral.herokuapp.com/launch; in the field
 labeled Shared cluster string and click the button to create my
 instance.  But then when I log into Cloudman the Initial Cluster
 configuration dialog is still appearing.
 
 I ran the same thing yesterday with an older share string and
 everything worked fine.
 
 Any ideas what could be going on?  I'm pretty stuck.
 
 Thanks,
 
 Greg
 
 
 This is all I see in the cluster status log (I entered my share string
 again on the dialog, the disk status says 0 / 0 and applications and
 data lights are yellow, and don't seem to progress):
 
 13:34:46 - Master starting
 13:34:50 - Retrieved file
 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
 'cm-808d863548acae7c2328c39a90f52e29' to
 'shared_instance_file_list.txt'.
 13:41:29 - Retrieved file
 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
 'cm-808d863548acae7c2328c39a90f52e29' to
 'shared_instance_file_list.txt'.
 13:41:30 - Retrieved file 'persistent_data.yaml' from bucket
 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'shared_p_d.yaml'.
 13:41:31 - Created a data volume 'vol-7f2cc105' of size 5GB from
 shared cluster's snapshot 'snap-cfa775ba'
 13:41:31 - Saved file 'persistent_data.yaml' to bucket
 'cm-c8c215c4c67525d91b3a2598f9e370f7'
 13:41:31 - Retrieved file 'persistent_data.yaml' from bucket
 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'pd.yaml'.
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Re: [galaxy-user] How to transfer files between two galaxy instances

[Dannon Baker]

The data is not a part of the workflow -- what you want is a history export.

From the history you want to export, in the history menu, select Export to 
File.  This step may take a while depending on the size of your history.  
Navigate to the link to make sure it's done packaging the history.  If it 
isn't, you'll see Still exporting history your history; please check back 
soon.  If it is, a download will automatically start.  You can save this, or 
just cancel the download (if it's large).

Once the data is ready (the link works), on the destination Galaxy instance, 
select Import from File in the history menu.  Put in your link.

This should migrate the entire history.

On May 29, 2012, at 12:08 PM, shamsher jagat wrote:

 Ok. Perhaps I am not understanding the process- I am not making any head way 
 in transfering the data from one Galaxy instance to other. I have uploaded 
 some files in Rutsch lab galaxy instance and have url 
 http://galaxy.tuebingen.mpg.de/workflow/for_direct_import?id=9b305a114b324ccf
  
 Nothing is happening. Is it possible that some one from Galaxy team can 
 enlist steps of - how to transfer files (data) from one galaxy instance to 
 other please, considering me as a beginer. Thanks. Sorry for pushing this 
 question.
  
 Vasu
 On Fri, May 25, 2012 at 11:33 AM, Dannon Baker dannonba...@me.com wrote:
 Hi,
 
 Just wanted to add a few clarifications here.  It definitely *is* currently 
 possible to transfer a workflow from one instance to another instance that 
 does not have (some or all) of the tools for a particular workflow.
 
 The error you're running into No JSON object means that you likely have the 
 wrong link to your workflow.  The one you want is accessible via the workflow 
 context menu - Download or Export - URL for importing into another galaxy.  
 Or, you could just download the raw file if you want and upload that as you 
 figured out.  The format of the correct URL should look like this, note the 
 for_direct_import in the string:
 
 https://main.g2.bx.psu.edu/workflow/for_direct_import?id=53b7bf0869d3e7ee
 
 As a correction to what was previously said, I would not recommend stripping 
 out tools from an existing workflow prior to export.  When you upload the 
 workflow to a new instance, if tools aren't available you will see something 
 like the following when you edit the workflow, which specifies that the tool 
 is not found:
 
 PastedGraphic-1.png
 
 And at this point the unrecognized tools can be installed if it's your galaxy 
 server, or if you wish, removed from the workflow via the editor.  This must 
 be done before the workflow will be usable.
 
 Lastly, workflows don't contain any data, just the organization and 
 parameters of steps for a process.  What it sounds like you're looking for 
 (to get your data there as well) is a history export, which is available 
 through the menu at the top of your history as Export to File.
 
 -Dannon
 
 
 On May 24, 2012, at 4:06 PM, shamsher jagat wrote:
 
 Thanks Jen for the update. I tried following:
 Go to Ratsch Galaxy instance  workflow make work flow accessible via link
 Go to galaxy Penn server
 Workflow import workflow URL galaxy UR
  
 error is
  The data content does not appear to be a Galaxy workflow.
 Exception: No JSON object could be decoded: line 1 column 0 (char 0)
  
 I also downloaded the file from Ratsch serever saved on computer and  use 
 option of Choose file under import galaxy flow it importe dthe file afetr a 
 while and when I opened workflow there was no data only steps of the 
 workflow were there.
  
 Do you have any suggestion wheer I am doing something wrong.
  
 Thanks
 
 

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Re: [galaxy-user] How to transfer files between two galaxy instances

[Dannon Baker]

Hi,Just wanted to add a few clarifications here. It definitely *is* currently possible to transfer a workflow from one instance to another instance that does not have (some or all) of the tools for a particular workflow.The error you're running into "No JSON object" means that you likely have the wrong link to your workflow. The one you want is accessible via the workflow context menu - Download or Export - URL for importing into another galaxy. Or, you could just download the raw file if you want and upload that as you figured out. The format of the correct URL should look like this, note the "for_direct_import" in the string:https://main.g2.bx.psu.edu/workflow/for_direct_import?id=53b7bf0869d3e7eeAs a correction to what was previously said, I would not recommend stripping out tools from an existing workflow prior to export. When you upload the workflow to a new instance, if tools aren't available you will see something like the following when you edit the workflow, which specifies that the tool is not found:And at this point the unrecognized tools can be installed if it's your galaxy server, or if you wish, removed from the workflow via the editor. This must be done before the workflow will be usable.Lastly, workflows don't contain any data, just the organization and parameters of steps for a process. What it sounds like you're looking for (to get your data there as well) is a history export, which is available through the menu at the top of your history as "Export to File".-DannonOn May 24, 2012, at 4:06 PM, shamsher jagat wrote:Thanks Jen for the update. I tried following:Go to Ratsch Galaxy instance  workflow make work flow accessible via linkGo to galaxy Penn serverWorkflow import workflow URL galaxy URerror isThe data content does not appear to be a Galaxy workflow.Exception: No JSON object could be decoded: line 1 column 0 (char 0)I also downloaded the file from Ratsch serever saved on computer and use option of Choose file under import galaxy flow it importe dthe file afetr a while and when I opened workflow there was no data only steps of the workflow were there.Do you have any suggestion wheer I am doing something wrong.Thanks___
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Re: [galaxy-user] cuff... errors

[Dannon Baker]

There was a temporary cluster issue, but it looks like jobs are running again.  
Try resubmitting your jobs now, and they should succeed.

-Dannon

On May 1, 2012, at 8:30 PM, Jeremy Coate wrote:

 Hi all,
 FYI, I've gotten the same error recently when trying to run Bowtie (using 
 Galaxy Main).
 Jeremy
 
 On Tue, May 1, 2012 at 4:37 PM, Richard Mark White whit...@yahoo.com wrote:
 Hi,
 Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job 
 output not returned by PBS: the output datasets were deleted while the job 
 was running, the job was manually dequeued or there was a cluster error.
 
 is there a system issue or something with my data?
 
 r
 
 
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Re: [galaxy-user] Problems starting Galaxy Cloudman

[Dannon Baker]

Greg,

The problem here is that the galaxy update failed to merge a change to run.sh 
because of minor customizations it has.  We'll have a long term fix out for 
this soon, but for now what you can do is ssh in to your instance and update 
run.sh yourself prior to restarting galaxy.  All you need to do is add 
'migrated_tools_conf.xml.sample' to the SAMPLES in 
/mnt/galaxyTools/galaxy-central/run.sh, execute `sh run.sh --run-daemon` (or 
restart galaxy again from the admin page) and you should be good to go.

That new AMI you're seeing is not owned by the Galaxy Team, and we don't 
actually know who made it.  Keep using the same galaxy-cloudman-2011-03-22 for 
now (and we'll always have the most up-to-date AMI listed at 
usegalaxy.org/cloud).  Because of Cloudman's modular volume design almost 
nothing resides on the AMI itself, so we can (and do) update the tools and 
index volumes without having to touch it.  So while the AMI reflects a date of 
almost a year old, the galaxy tools volume (and thus the actual Galaxy instance 
you're running) has been updated much more recently.

One last note- if you're updating and copying your tools in every time, you may 
want to try using the 'Persist changes' functionality available in the Cloudman 
admin panel.  Once you've set your instance up how you want, if you click 
'Persist changes to galaxyTools', it'll create a custom snapshot of your tools 
volume that will be used from that point forward with this instance.

Let me know if you have any more issues,

-Dannon

On Mar 9, 2012, at 2:53 AM, Greg Edwards wrote:

 Hi,
 
 I'm trying to restart my Galaxy Cloudman service, using the same approach 
 that has been successful over the last couple of months ..
 
  - launch AMI 861460482541/galaxy-cloudman-2011-03-22 as m1.large
  - update from Cloudman console
  - copy in my tools etc etc
  - restart
  - away we go, all works
 
 However today the update fails, the log says ...
 
 /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
  RuntimeWarning: __builtin__.file size changed, may indicate binary 
 incompatibility
   from csamtools import *
 python path is: 
 /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
  /mnt/galaxyTools/galaxy-central/eggs/boto-2.2.2-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
  
 /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
  
 /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
  /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, 
 /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
  /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/g!
 alaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, 
/mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, 
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, 
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
 Traceback (most recent call last):
   File /mnt/galaxyTools/galaxy-central/lib/galaxy/web/buildapp.py, line 82, 
 in app_factory
 app = UniverseApplication( global_conf = global_conf, **kwargs )
   File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 24, in 
 __init__
 self.config.check()
   File /mnt/galaxyTools/galaxy-central/lib/galaxy/config.py, line 243, in 
 check
 tree = parse_xml( config_filename )
   File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line 
 105, in parse_xml
 tree = ElementTree.parse(fname)
   File 
 /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py,
  line 859, in parse
 tree.parse(source, parser)
   File 
 /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py,
  line 576, in parse
 source = 

Re: [galaxy-user] error uploading from ftp site

[Dannon Baker]

This should be fixed as of yesterday afternoon.  Are you still having issues?

-Dannon

On Mar 1, 2012, at 11:28 AM, Keith E. Giles wrote:

 All of a sudden I can not upload any files from the FTP server.  The files 
 upload into my ftp directory fine, but when I try to upload them into galaxy, 
 I get the following error:
 
 Error executing tool: normalize() argument 2 must be unicode, not str
 
 any ideas?
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Re: [galaxy-user] Megablast question

[Dannon Baker]

Noa has the right idea, but if you're asking for how to split a dataset into 
two non-overlapping halves you'll want to use Select First and Select Last, 
instead of random lines.  Get an accurate line count from your file using the 
Line/Word/Character count tool and then split it right in the middle using 
select first/last.

-Dannon

On Feb 16, 2012, at 2:35 PM, Noa Sher wrote:

 Hi Scott
 I  never used megablast so what i am writing is true of just any fasta file 
 (so if there is anything quirky in megablast that i dont know about, 
 apologies!):
   • Take your fasta file and convert to tabular (under fasta 
 manipulation - this will make it go to one line per record).
   • Then randomly choose whatever number of reads you want using select 
 random lines from a file under the text maniupulation tab.
   • Then convert the tabular file back to fasta. (under the fasta 
 manipulation tab)
 noa
 On 16/02/2012 19:31, Scott Tighe wrote:
 Hi all
 
 When using Galaxy megablast, is there a simple way to reduce my FASTA files 
 from 23 million reads to 1/2 that size and submit to megablast separately?
 
 Thanks
 -- 
 Scott Tighe
 Advanced Genome Technology Lab
 Vermont Cancer Center at the University of Vermont
 149 Beaumont Avenue
 Health Science Research Bd RM 305
 Burlington Vermont USA 05405
 lab  802-656-AGTC (2482)
 cell 802-999-
 
 
 
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Re: [galaxy-user] Production environment

[Dannon Baker]

On Feb 10, 2012, at 3:28 AM, David Castillo wrote:

   • I haven't been able to 'Edit' Workflows like in the public server, I 
 have been able to create them, but once I try to edit them it just attempts 
 to load the 'Workflow Editor' but it never does. How can I solve this? Do I 
 have to configure something before attempting to do this?

This should work out of the box without any extra configuration.  Do you see 
any errors(failure to load a resource, javascript errors, etc) when you attempt 
to load the editor?  My hunch is that galaxy.workflow_editor.canvas.js isn't 
being found, perhaps due to a proxy configuration being not quite right.  Is 
this galaxy instance set up behind apache or nginx?

-Dannon
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Re: [galaxy-user] A simple operation didn't work out

[Dannon Baker]

Hi Jiwen,

The way the filter expression evaluates, you need to specify that you're 
matching on the string '19', and not the numerical value 19.  Everything should 
work if you rerun with the filter condition:
c1=='19'

Thanks!

Dannon



On Feb 1, 2012, at 9:56 AM, 杨继文 wrote:

  Hi All,
 I got a bit disappointed when I failed in the following operation which seems 
 to be simple.
 
 I uploaded mouse annotation/reference gene sets (GTF format) to Galaxy. The 
 file is located at ftp://ftp.ensembl.org/pub/release-65/gtf/mus_musculus/.
  
 As far as I know, GTF file is tab delimited, thus I used Filter and Sort 
 --filter With following condition:C1 == 19 .
 column 1 is where chromosomes are located. I want to pick up all lines which 
 belong to chromosome19.
 However, I only got an empty file. 
 
 I know this is not a bit issue to discuss here. But I still  hope  you can 
 help me figure out what 's wrong.
 Thanks
 Jiwen
 
 
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Re: [galaxy-user] The size of the history

[Dannon Baker]

Jiwen,

After purging datasets, the history size update has a bit of a delay.  Let us 
know if you find that after a while it hasn't recalculated to what you expect 
the value to be.

-Dannon


On Feb 1, 2012, at 4:21 PM, 杨继文 wrote:

 Hi all,
 First I would like to thank you for your fast replies to my questions.
 As you know, at top right corner of Galaxy window, there are records of the 
 history size and how many percentage of memory space has been used. I found 
 that the number in the records only increases, but doesn't decrease after I 
 delete files permanently.
 DId I miss something? How to let the record show the real size of the 
 histories?
 Thanks in advance.
 Greetings,
 Jiwen
 
 
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Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

[Dannon Baker]

It's the other nginx.conf at /opt/galaxy/pkg/nginx/conf/nginx.conf, I don't 
think that one you found is used.  And it isn't explicitly set at all 
currently, so the default 1m gets applied.

And, to reload with the modified config, I think this should do the trick (as 
the ubuntu user)-

sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`

-Dannon


On Jan 23, 2012, at 4:43 AM, Greg Edwards wrote:

 Hi Dannon,
 
 I found nginx.conf at  /opt/galaxy/pkg/nginx_upload_module-2.0.12/nginx.conf
 
 It contains ..
 
  client_max_body_size 100m;
 
 That looks like 100 Megabyte ?? but seems to result in 1 Megabyte. Can I set 
 it to 1m, or 1g ?
 
 Can't see how to restart nginx yet.
 
 Thanks,
 Greg E
 
 
 
 
 
 On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker dannonba...@me.com wrote:
 Hi Greg,
 
 This is a problem with the default client_max_body_size option in nginx being 
 set far too small in the nginx.conf on the cloud AMI.  It'll be fixed with 
 our next AMI update, but to fix it you have to edit the nginx.conf on your 
 cloud node to change the client_max_body_size to something more appropriate 
 for Galaxy uploads and then restart the nginx process.
 
 You'd have to do it for every instance, unfortunately, since that section of 
 the filesystem is not persisted after shutdown.  As a workaround the URL 
 upload will work correctly with any size file if you're able to host the file 
 you want to upload somewhere local, or you could use FTP upload and that 
 should also function correctly.
 
 -Dannon
 
 
 On Jan 23, 2012, at 4:09 AM, Greg Edwards wrote:
 
  Hi,
 
  I'm building a Galaxy Cloud implementation, and running into a problem 
  uploading data files  1 Mbyte, or 1,048,576 bytes.
 
  I've started Galaxy Cloudman and a single server, all according to to the 
  Wiki. I can upload fasta format files  1048756 bytes, and general CSV 
  format peptide files, and indeed junk data files built with variants of  
  jot -r -c 103 a z | rs -g 0 100 junk .
 
  If I upload files (via the built-in Get Data / Upload Files From Your 
  Computer) that are  than approx 2^20 bytes, the upload just hangs in the 
  History and never completes.
 
  These files upload fine to a local Galaxy server, and to Galaxy Main. On 
  the Galaxy local server, they run fine with my custom proteomics code. 
  Ditto on the Cloud galaxy server when the (smaller than 1 Mbtye) files 
  successfully upoad.
 
  I can't see anthing useful in the logs, but I'm not sure which logs I 
  should be looking at. I'm just looking at tyhe logs presented on the 
  Cloudman admin page.
 
  logs.png
 
  My environment is Mac, OS X 10.6.8. My data files are terminated with /n, 
  but the problem manifests the same with Windows style /r/n files.
 
  I'll leave it at that in the hope this is a ridiculously simple probelm and 
  needs no more description ! If not, please let me know the logs I should 
  look at and whatever else I should check.
 
  Many thanks,
  Greg E
 
  --
  Greg Edwards,
  Port Jackson Bioinformatics
  gedwar...@gmail.com
 
  ___
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  Galaxy analysis and other features on the public server
  at usegalaxy.org.  Please keep all replies on the list by
  using reply all in your mail client.  For discussion of
  local Galaxy instances and the Galaxy source code, please
  use the Galaxy Development list:
 
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  please use the interface at:
 
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 -- 
 Greg Edwards,
 Port Jackson Bioinformatics
 gedwar...@gmail.com
 

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Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

[Dannon Baker]

Great, glad it worked for you!

And, once we release a new AMI, it'll be fixed retroactively.  That is, you'll 
be able to use your existing cloud setup with the new AMI and it should just 
work.

-Dannon


On Jan 23, 2012, at 5:35 AM, Greg Edwards wrote:

 Dannon,
 
 Cool, that seems to have worked. I set 
 
 server {
 listen   80;
 client_max_body_size 500m;
 
 in  /opt/galaxy/pkg/nginx/conf/nginx.conf
 
 and issued   sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`
 
 and it's uploading my test files of 2mb to 25mb ok.
 
 I think it will be easier to do that in my Cloud setup than instruct my (not 
 very computer keen) wet-lab Proteomist clients how to use a subsidiary FTP 
 package, easy though that is. But I'll try the FTP approach too for 
 compariosn.
 
 Thanks,
 Greg E
 
 
 On Mon, Jan 23, 2012 at 8:58 PM, Dannon Baker dannonba...@me.com wrote:
 It's the other nginx.conf at /opt/galaxy/pkg/nginx/conf/nginx.conf, I don't 
 think that one you found is used.  And it isn't explicitly set at all 
 currently, so the default 1m gets applied.
 
 And, to reload with the modified config, I think this should do the trick (as 
 the ubuntu user)-
 
 sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`
 
 -Dannon
 
 
 On Jan 23, 2012, at 4:43 AM, Greg Edwards wrote:
 
  Hi Dannon,
 
  I found nginx.conf at  /opt/galaxy/pkg/nginx_upload_module-2.0.12/nginx.conf
 
  It contains ..
 
   client_max_body_size 100m;
 
  That looks like 100 Megabyte ?? but seems to result in 1 Megabyte. Can I 
  set it to 1m, or 1g ?
 
  Can't see how to restart nginx yet.
 
  Thanks,
  Greg E
 
 
 
 
 
  On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker dannonba...@me.com wrote:
  Hi Greg,
 
  This is a problem with the default client_max_body_size option in nginx 
  being set far too small in the nginx.conf on the cloud AMI.  It'll be fixed 
  with our next AMI update, but to fix it you have to edit the nginx.conf on 
  your cloud node to change the client_max_body_size to something more 
  appropriate for Galaxy uploads and then restart the nginx process.
 
  You'd have to do it for every instance, unfortunately, since that section 
  of the filesystem is not persisted after shutdown.  As a workaround the URL 
  upload will work correctly with any size file if you're able to host the 
  file you want to upload somewhere local, or you could use FTP upload and 
  that should also function correctly.
 
  -Dannon
 
 
  On Jan 23, 2012, at 4:09 AM, Greg Edwards wrote:
 
   Hi,
  
   I'm building a Galaxy Cloud implementation, and running into a problem 
   uploading data files  1 Mbyte, or 1,048,576 bytes.
  
   I've started Galaxy Cloudman and a single server, all according to to the 
   Wiki. I can upload fasta format files  1048756 bytes, and general CSV 
   format peptide files, and indeed junk data files built with variants of  
   jot -r -c 103 a z | rs -g 0 100 junk .
  
   If I upload files (via the built-in Get Data / Upload Files From Your 
   Computer) that are  than approx 2^20 bytes, the upload just hangs in the 
   History and never completes.
  
   These files upload fine to a local Galaxy server, and to Galaxy Main. On 
   the Galaxy local server, they run fine with my custom proteomics code. 
   Ditto on the Cloud galaxy server when the (smaller than 1 Mbtye) files 
   successfully upoad.
  
   I can't see anthing useful in the logs, but I'm not sure which logs I 
   should be looking at. I'm just looking at tyhe logs presented on the 
   Cloudman admin page.
  
   logs.png
  
   My environment is Mac, OS X 10.6.8. My data files are terminated with /n, 
   but the problem manifests the same with Windows style /r/n files.
  
   I'll leave it at that in the hope this is a ridiculously simple probelm 
   and needs no more description ! If not, please let me know the logs I 
   should look at and whatever else I should check.
  
   Many thanks,
   Greg E
  
   --
   Greg Edwards,
   Port Jackson Bioinformatics
   gedwar...@gmail.com
  
   ___
   The Galaxy User list should be used for the discussion of
   Galaxy analysis and other features on the public server
   at usegalaxy.org.  Please keep all replies on the list by
   using reply all in your mail client.  For discussion of
   local Galaxy instances and the Galaxy source code, please
   use the Galaxy Development list:
  
http://lists.bx.psu.edu/listinfo/galaxy-dev
  
   To manage your subscriptions to this and other Galaxy lists,
   please use the interface at:
  
http://lists.bx.psu.edu/
 
 
 
 
  --
  Greg Edwards,
  Port Jackson Bioinformatics
  gedwar...@gmail.com
 
 
 
 
 
 -- 
 Greg Edwards,
 Port Jackson Bioinformatics
 gedwar...@gmail.com
 

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Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

[Dannon Baker]

Yes, galaxyData is the only persistent volume you have in your data only 
cluster, so everything should go there.  SCP should work for getting data 
there, unless the file is already hosted somewhere in which case wget is 
probably a better choice.

And yes, FTP is configured specifically for Galaxy uploads and is unavailable 
in the case of a non-galaxy cluster.  The usernames used for logging in, etc, 
come straight from the Galaxy database.

On Jan 12, 2012, at 12:56 PM, mailing list wrote:

 Hi guys,
 
 Another related question.  So if I need a large data set for my
 program to run on, should that also be stored in GalaxyData?  What is
 the best way to get the data on there?
 
 I saw something about FTP but it seemed kind of confusing.  Also I
 chose the data cluster option so I don't think I have an instance of
 Galaxy running.  Is that what would do the FTP?
 
 Thanks again,
 
 Greg

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Re: [galaxy-user] CloudMan - Persist changes to file system is not a hyperlink / clickable

[Dannon Baker]

For sharing a cluster (of any kind) just click the sharing icon ()next to the cluster name and the dialog that pops up will walk you through the next steps.-DannonOn Jan 11, 2012, at 7:27 AM, mailing list wrote:So how do I get a share string for /mnt/galaxyData?Thanks again,GregOn Tue, Jan 10, 2012 at 4:16 PM, Dannon Baker dannonba...@me.com wrote:Sorry, I should have specified before -- /mnt/galaxyData is automatically persisted, as it is assumed (and used behind the scenes in the case of a Galaxy Cluster) that this is where data will be kept. It's only /mnt/galaxyTools or /mnt/galaxyIndices that need individual flagging for persistence.So, /mnt/galaxyData *is* safe to use for your own customizations and will be persisted automatically with no additional steps required on your part.-DannonOn Jan 10, 2012, at 4:02 PM, mailing list wrote:I'm following the instructions here:http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20CloudI ssh'd in and just made this change:cd /mnt/galaxyDatasudo git clone git://github.com/JaneliaSciComp/msg.gitNow I want to persist it, but as my subject line says, I don't seem tohave the option in the admin.Thanks,Greg___The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org. Please keep all replies on the list byusing "reply all" in your mail client. For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list:http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at:http://lists.bx.psu.edu/___
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Re: [galaxy-user] Data upload

[Dannon Baker]

Ateeq,

The preferred method for uploading large files (that aren't already hosted 
somewhere) is FTP.  See the instructions here: 
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

We don't generally provide specific analysis pipelines, rather the tools for 
composing them, though you're welcome to look through the shared workflows, 
histories, and pages (See Shared Data in Galaxy) for examples and perhaps 
someone else will chime in with their experiences analyzing bacterial 
transcriptomes.

Lastly, try not to piggyback on unrelated threads (as in your other email).  It 
makes tracking email replies more difficult.

-Dannon

On Jan 9, 2012, at 10:30 AM, Ateequr Rehman wrote:

 Dear galaxy Users
 
 I am very very new to galaxy, will be highly obliged if some one could help 
 me to find the way to analyse bacterial tramnscriptome. in the first step 
 itself , i am having trouble to upload files...
 
 Does any one knows how to generate URL to upload data, my fastq files are 
 about 3 gb each, 
 
 Is there any specific pipeline to analyse bacterial transcriptome
 
 Thanking all of you
 
 Ateeq
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Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

[Dannon Baker]

Correct to the first point.

The space available to /mnt/galaxyTools is not configurable through the 
interface, though you could manually resize a volume if you did need more room. 
 /mnt/galaxyData is the volume referred to in the dialogs you're seeing.

-Dannon

On Jan 10, 2012, at 2:53 PM, mailing list wrote:

 Thanks.  So if I just want to run my own program that uses SGE, it
 sounds like I shouldn't need a Galaxy instance.  Is that right?
 
 Does the storage space parameter control how much space is at 
 /mnt/galaxyTools?
 
 -Greg
 
 On Tue, Jan 10, 2012 at 2:50 PM, Dannon Baker dannonba...@me.com wrote:
 Data Cluster only configures a persistent data volume and SGE.  Galaxy 
 Cluster includes a running Galaxy instance in addition to the persistent 
 data volume and SGE configuration components from the Data Cluster option.  
 The Galaxy Cluster option is what most users will probably want to choose.
 
 How much space is absolutely dependent on your needs.  Keep in mind that you 
 can increase size later if necessary via the admin UI.  The maximum volume 
 size (per an amazon limit to EBS volume size) is currently 1TB.
 
 -Dannon
 
 
 On Jan 10, 2012, at 2:42 PM, mailing list wrote:
 
 Hi guys,
 
 When I first go to my cloudman page at public dns/cloud I get a
 dialog asking for some settings.
 
 What does the Galaxy Cluster choice do?  What does the Data Cluster
 choice do?  Why can't I choose both?  How much space should I
 allocate?
 
 Thanks,
 
 Greg
 
 Text of dialog:
 
 Galaxy Cluster: Galaxy application, available tools, reference
 datasets, SGE job manager, and a data volume. Specify the initial
 storage size (in Gigabytes):
 GBOK
 
 Share-an-Instance Cluster: derive your cluster form someone else's
 cluster. Specify the provided cluster share-string (for example,
 cm-0011923649e9271f17c4f83ba6846db0/shared/2011-08-19--21-00):
 Cluster share-string
 
 Data Cluster: a persistent data volume and SGE. Specify the initial
 storage size (in Gigabytes):
 GB
 
 Test Cluster: SGE only. No persistent storage is created.
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Re: [galaxy-user] CloudMan Launch Page - Hanging

[Dannon Baker]

It looks like you're trying to restart an existing cluster (same cluster name) 
that previously had galaxy included.  Is this the case?  If so, you'll need to 
start it in the same availability zone as the existing volumes.


On Jan 10, 2012, at 3:03 PM, mailing list wrote:

 The page seems to be loading now but I think I'm getting some weird
 behavior on my started instance.
 
 None of the services except SGE started up, and I see this under
 cluster status log on the main page:
 
* 19:57:11 - Retrieved file 'persistent_data.yaml' from bucket
 'cm-31bf91*22c1a276ece' to 'pd.yaml'.
* 19:57:11 - Master starting
* 19:57:11 - Completed initial cluster configuration.
* 19:57:27 - PostgreSQL data directory
 '/mnt/galaxyData/pgsql/data' does not exist (yet?)
* 19:57:27 - Prerequisites OK; starting service 'SGE'
* 19:57:32 - Configuring SGE...
* 19:57:41 - Successfully setup SGE; configuring SGE
* 19:58:16 - Attaching volume 'vol-35*58' to instance
 'i-ee7e298c' as device '/dev/sdg3' failed. Exception:
 EC2ResponseError: 400 Bad Request InvalidVolume.ZoneMismatchThe volume
 'vol-35d4f058' is not in the same availability zone as instance
 'i-ee*def-3ce4-4c41-8909-15e0*6e15
* 19:59:16 - Cannot detach volume 'vol-35d4f058' in state 'available'
* 20:00:17 - Cannot detach volume 'vol-35d4f058' in state 'available'
 # 20:01:19 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:19 - Cannot start service 'Postgres' because prerequisites are
 not yet satisfied.
 # 20:01:19 - Cannot start service 'Galaxy' because prerequisites are
 not yet satisfied.
 # 20:01:19 - Saved file 'persistent_data.yaml' to bucket
 'cm-31bf9*9ff78a*a276ece'
 # 20:01:19 - Trouble comparing local (/mnt/cm/post_start_script) and
 remote (post_start_script) file modified times: [Errno 2] No such file
 or directory: '/mnt/cm/post_start_script'
 # 20:01:24 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:24 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:01:41 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:41 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:01:57 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:57 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:02:14 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:02:14 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 
 
 (I masked some of the numbers in case they're sensitive)
 
 
 
 On Tue, Jan 10, 2012 at 2:15 PM, mailing list margeem...@gmail.com wrote:
 Hi guys,
 
 Is the launch page down today?
 
 https://biocloudcentral.herokuapp.com/launch
 
 It seems to just hang for me and not load.
 
 Let me know if there's anything I can do
 
 Thanks
 
 Greg
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Re: [galaxy-user] CloudMan Launch Page - Hanging

[Dannon Baker]

In your AWS management console delete the s3 bucket containing the cluster 
information.  In the s3 viewer, the .clusterName file reflects the name of the 
cluster.

You'll probably also want to delete the EBS data volume associated with that 
cluster, though electing to keep this won't prevent starting a new cluster.  
These volume id's are in the persistent_data.yaml file in the primary bucket 
(that you're deleting).

And then to avoid this in the future, when you want to permanently kill a 
cluster select the deletion option at cluster termination to remove the bucket 
and volumes permanently.

-Dannon

On Jan 10, 2012, at 3:18 PM, mailing list wrote:

 Yes, I did use the same name.  I thought once I terminated everything
 would be gone.
 
 So how do I make a clean start?
 
 Thanks,
 
 Greg
 
 On Tue, Jan 10, 2012 at 3:08 PM, Dannon Baker dannonba...@me.com wrote:
 It looks like you're trying to restart an existing cluster (same cluster 
 name) that previously had galaxy included.  Is this the case?  If so, you'll 
 need to start it in the same availability zone as the existing volumes.
 
 
 On Jan 10, 2012, at 3:03 PM, mailing list wrote:
 
 The page seems to be loading now but I think I'm getting some weird
 behavior on my started instance.
 
 None of the services except SGE started up, and I see this under
 cluster status log on the main page:
 
* 19:57:11 - Retrieved file 'persistent_data.yaml' from bucket
 'cm-31bf91*22c1a276ece' to 'pd.yaml'.
* 19:57:11 - Master starting
* 19:57:11 - Completed initial cluster configuration.
* 19:57:27 - PostgreSQL data directory
 '/mnt/galaxyData/pgsql/data' does not exist (yet?)
* 19:57:27 - Prerequisites OK; starting service 'SGE'
* 19:57:32 - Configuring SGE...
* 19:57:41 - Successfully setup SGE; configuring SGE
* 19:58:16 - Attaching volume 'vol-35*58' to instance
 'i-ee7e298c' as device '/dev/sdg3' failed. Exception:
 EC2ResponseError: 400 Bad Request InvalidVolume.ZoneMismatchThe volume
 'vol-35d4f058' is not in the same availability zone as instance
 'i-ee*def-3ce4-4c41-8909-15e0*6e15
* 19:59:16 - Cannot detach volume 'vol-35d4f058' in state 'available'
* 20:00:17 - Cannot detach volume 'vol-35d4f058' in state 'available'
 # 20:01:19 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:19 - Cannot start service 'Postgres' because prerequisites are
 not yet satisfied.
 # 20:01:19 - Cannot start service 'Galaxy' because prerequisites are
 not yet satisfied.
 # 20:01:19 - Saved file 'persistent_data.yaml' to bucket
 'cm-31bf9*9ff78a*a276ece'
 # 20:01:19 - Trouble comparing local (/mnt/cm/post_start_script) and
 remote (post_start_script) file modified times: [Errno 2] No such file
 or directory: '/mnt/cm/post_start_script'
 # 20:01:24 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:24 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:01:41 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:41 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:01:57 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:01:57 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 # 20:02:14 - STATUS CHECK: File system named 'galaxyData' is not
 mounted. Error code 0
 # 20:02:14 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
 does not exist (yet?)
 
 
 (I masked some of the numbers in case they're sensitive)
 
 
 
 On Tue, Jan 10, 2012 at 2:15 PM, mailing list margeem...@gmail.com wrote:
 Hi guys,
 
 Is the launch page down today?
 
 https://biocloudcentral.herokuapp.com/launch
 
 It seems to just hang for me and not load.
 
 Let me know if there's anything I can do
 
 Thanks
 
 Greg
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 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
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Re: [galaxy-user] CloudMan - Galaxy - How does sharing work?

[Dannon Baker]

Greg-

When you make changes to the EBS volumes of a galaxy cloudman instance and 
choose 'persist' from the admin panel, an EBS snapshot is taken.  The next time 
you start an instance up, instead of creating the EBS volume from the base 
snapshot that we distribute, it is created from your own customized snapshot.

The share string is actually a handle to a cloudman s3 bucket.  That bucket 
contains all of the configuration information for your cluster and 
customizations.  You can look at your own buckets to see the information saved, 
if you'd like.  When the share-an-instance configuration steps happen and 
snapshots are taken, privileges are set to allow others to access those 
snapshots.

Since the customizations you make to galaxy are stored as an EBS snapshot, this 
does carry an extra cost.  See more information about EBS snapshots at 
http://aws.amazon.com/ebs/.

And, lastly, if you're *really* interested in the nuts and bolts of how it 
happens, see the source here: 
https://bitbucket.org/galaxy/cloudman/src/tip/cm/util/master.py#cl-859

-Dannon



On Jan 9, 2012, at 9:26 AM, mailing list wrote:

 I was wondering how the sharestring feature works?
 
 Enis mention it a little bit here:
 http://biostar.stackexchange.com/questions/15467/galaxy-cloudman-best-way-to-customize-and-share-cloudman/15481#15481
 
 So as I understand it, I do my customizations and persist them, and
 then I get a sharestring so others can load my customizations.
 
 How does this work behind the scenes?
 
 Also where are my customizations stored?  Am I charged by Amazon for
 storing them?  How do others have permissions to pull them from my
 Amazon account?
 
 (I'm new to all of this, sorry if my questions are obvious)
 
 -Greg
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 at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] Cucumber genome

[Dannon Baker]

Changlong,

Lastz (and many other tools) allow you to select a reference from your history 
instead of picking one of Galaxy's built-in references.  To do this, upload 
your reference and then when you run Lastz select in your history for the 
reference location, and pick your uploaded file as the reference dataset.

-Dannon


On Dec 9, 2011, at 4:44 AM, changlong wen wrote:

 Hi,
 
 In the NGS mapping option with lastz I cannot find the Cucumber genome.
 Could you please make this reference genome available? 
 Or we have the reference sequence. How to add them in in the local server?
 Many thanks.
 
 Have a good day.
 
 Best regards
 changlong
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Re: [galaxy-user] [galaxy-dev] Urgent help needed

[Dannon Baker]

I don't know anything about the tool or parameters in question , but it looks 
like the expected output filename is well formatted enough that you can derive 
it from the input filename and parameters.

You could write a small python wrapper to grant you full control over 
manipulating output files and finding/renaming them as you like, or, you could 
maybe try something like (and I have not tried this at all myself and have no 
idea what your parameters mean)  
from_work_dir=${input1}reads_l_${parameter1}_${parameter2}_CNTGS_DIST0_EM20.txt

Good luck-

Dannon

On Dec 5, 2011, at 3:52 PM, Toqa Manasrah wrote:

 Thank you so much Dannon.
 I appreciate your help but I need some more clarification.
 
 in the tool I am integrating (which is java classes) if the input parameters 
 are
 
 ./main.bash  eps0.3_40reads.fa  population10_ref.fa 15 6 120
 
 Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt
 
 As u notice the output file name is not specified in teh command line, and 
 actually I dont have the source files to go over this naming restriction.
 
 how I can use from_work_dir attribute to tell galaxy this the file to display?
 
 note: there are 11 output files and I am interested in this one only 
 ..._CNTGS_DIST0_EM20.txt
 
 
 any other method to overcome such problem  
 
 I have presentation tomorrwo. hope things will work fine.
 
 Thank you,
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Monday, December 05, 2011 2:41 PM
 To: Toqa Manasrah
 Subject: Re: [galaxy-dev]  Urgent help needed
 
 Sure.  See the link in my previous email 
 (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for 
 the data section for an explanation of the attributes available to you.  
 For an example of a tool that uses the from_work_dir element, see the 
 cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install.
 
 -Dannon
 
 
 On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote:
 
 Thank you Dannon,
 I mean the first choice. no way to specify the output name in tool and it 
 has many putputs but I am intereseted in one only.
 
 Actually I dont know to use this attribute from_work_dir and I cant find 
 help. can u help plz?
 
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Monday, December 05, 2011 1:54 PM
 To: Toqa Manasrah
 Cc: galaxy-...@bx.psu.edu dev; Jennifer Jackson; galaxy-user
 Subject: Re: [galaxy-dev]  Urgent help needed
 
 Toqa,
 
 Just to make sure I've understood your question: the problem is that a tool 
 that you're trying to wrap doesn't provide a way to specify a particular 
 output filename?  Take a look at the from_work_dir attribute of a data 
 element.
 
 Or are you asking how to define outputs in general?  For that, see the wiki 
 at 
 http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set
 
 Lastly, for new questions please start new email threads, instead of 
 replying to old ones.  This makes it much easier for us to track our 
 responses and make sure people get appropriate help.
 
 -Dannon
 
 
 On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:
 
 Hi Everybody,
 I am running a tool which is not defining the output file name as parameter.
 the tool is running and I can see the output file in the history directory 
 but not in the history frame.
 
 how could I solve the problem? I should see and download the output file 
 from the history but I see an error message instead. the error message not 
 a real error but rather galaxy cannot figure out which file to display?
 
 your help is appreciated,
 
 
 
 From: Jennifer Jackson [j...@bx.psu.edu]
 Sent: Tuesday, November 08, 2011 8:22 AM
 To: Toqa Manasrah
 Cc: Galaxy Dev
 Subject: Re: [galaxy-dev] Installing Galaxy on local server
 
 Hello Tuqa,
 
 Galaxy will not stop by itself. That said, you will want to monitor the
 instance and any associated cluster, just as you would any other
 important processes.
 
 Please send all follow-up with a cc to the mailing list (reply-all).
 The development community is a great resource for administrative advice
 and they may have more to add to this reply, i.e. how stable they have
 found Galaxy to be under various conditions.
 
 Best,
 
 Jen
 Galaxy team
 
 On 11/8/11 4:01 AM, Toqa Manasrah wrote:
 Thank you so much,
 
 I did the installation and I ran it under my server.
 I have one thing concerning about now. if u can help plz.
 
 how to run Galaxy in such way that the html interface will continuously 
 working and available for all users visiting the page?
 
 i mean how to guarantee that the sh run.sh will keep running without any 
 interrupt?
 
 Thank you,
 Tuqa
 
 
 From: Jennifer Jackson [j...@bx.psu.edu]
 Sent: Thursday, November 03, 2011 6:47 PM
 To: Toqa Manasrah
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Installing Galaxy on local server
 
 Hello Toqa

Re: [galaxy-user] [galaxy-dev] Urgent help needed

[Dannon Baker]

Toqa,

Just to make sure I've understood your question: the problem is that a tool 
that you're trying to wrap doesn't provide a way to specify a particular output 
filename?  Take a look at the from_work_dir attribute of a data element.

Or are you asking how to define outputs in general?  For that, see the wiki at 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set

Lastly, for new questions please start new email threads, instead of replying 
to old ones.  This makes it much easier for us to track our responses and make 
sure people get appropriate help.

-Dannon


On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:

 Hi Everybody,
 I am running a tool which is not defining the output file name as parameter.
 the tool is running and I can see the output file in the history directory 
 but not in the history frame.
 
 how could I solve the problem? I should see and download the output file from 
 the history but I see an error message instead. the error message not a real 
 error but rather galaxy cannot figure out which file to display?
 
 your help is appreciated,
 
 
 
 From: Jennifer Jackson [j...@bx.psu.edu]
 Sent: Tuesday, November 08, 2011 8:22 AM
 To: Toqa Manasrah
 Cc: Galaxy Dev
 Subject: Re: [galaxy-dev] Installing Galaxy on local server
 
 Hello Tuqa,
 
 Galaxy will not stop by itself. That said, you will want to monitor the
 instance and any associated cluster, just as you would any other
 important processes.
 
 Please send all follow-up with a cc to the mailing list (reply-all).
 The development community is a great resource for administrative advice
 and they may have more to add to this reply, i.e. how stable they have
 found Galaxy to be under various conditions.
 
 Best,
 
 Jen
 Galaxy team
 
 On 11/8/11 4:01 AM, Toqa Manasrah wrote:
 Thank you so much,
 
 I did the installation and I ran it under my server.
 I have one thing concerning about now. if u can help plz.
 
 how to run Galaxy in such way that the html interface will continuously 
 working and available for all users visiting the page?
 
 i mean how to guarantee that the sh run.sh will keep running without any 
 interrupt?
 
 Thank you,
 Tuqa
 
 
 From: Jennifer Jackson [j...@bx.psu.edu]
 Sent: Thursday, November 03, 2011 6:47 PM
 To: Toqa Manasrah
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Installing Galaxy on local server
 
 Hello Toqa,
 
  From your description, this sounds like a local installation for the
 Galaxy instance itself. Then you can add on a cluster (local or cloud)
 as needed.
 
 Help is under Deploy Galaxy at http://wiki.g2.bx.psu.edu/
 Also see the Tool Shed at http://wiki.g2.bx.psu.edu/Tool%20Shed
 
 Hopefully the documentation is helpful,
 
 Best,
 
 Jen
 Galaxy team
 
 On 11/3/11 9:40 AM, Toqa Manasrah wrote:
 Hello,
 
 I am a graduate student at GSU. I am looking for installing GALAXY on
 our local server http://alla.cs.gsu.edu/~software. as a result I like my
 server homepage start with the GALAXY interface, like this one:
 http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
 software tolls that we developed in ourdepartment. my primary question
 is which option Ihave to choose: Local or cloud?
 
 looking forward for your help and directions.
 
 Thank you.
 
 Tuqa
 
 
 
 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
 
http://lists.bx.psu.edu/
 
 --
 Jennifer Jackson
 http://usegalaxy.org
 http://galaxyproject.org/wiki/Support
 
 
 --
 Jennifer Jackson
 http://usegalaxy.org
 http://galaxyproject.org/wiki/Support
 
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at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] Amazon AMI

[Dannon Baker]

I see in your screenshot that the security group is only listed as default.  
Have you created the required security group as described in 
http://wiki.g2.bx.psu.edu/Admin/Cloud ?  If so, make sure you select that 
security group when you launch the instance, and my guess is that it'll solve 
your problem.

Thanks for trying Galaxy on the Cloud!

-Dannon


On Oct 28, 2011, at 10:51 PM, Daniel Muehlschlegel wrote:

 Hi,
 
 I installed the Amazon Galaxy CloudMan today but am not able to load any of 
 the Galaxy AMIs. The AMI on the user galaxy webpage does not exist, but 3 
 AMIs do. I tried the 2 most current ones and they don't load:
 710521EE-C6B4-43AB-B082-4461EAC78B9E.png
 
 
 It looks like everything is fine on the Amazon side:
 
 0A021174-E68A-468C-A4DE-A60B9D854F70.png 
 
 EBDE5EB8-2C29-4F13-AA0F-3D8BAC5D36DB.png
 
 Thanks for your help,
 
 Danny
 710521EE-C6B4-43AB-B082-4461EAC78B9E.png0A021174-E68A-468C-A4DE-A60B9D854F70.pngEBDE5EB8-2C29-4F13-AA0F-3D8BAC5D36DB.png___
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Re: [galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

[Dannon Baker]

Hi Marc,

Yes, if you change Bowtie settings to use from common to full, you'll see the 
entire parameter list, including Number of mismatches for SOAP-like alignment 
policy (-v):

-Dannon

On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote:

 Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in –v 
 alignment mode/ If so, what settings do I need to enter? Many thanks, Marc.
  
  
 ***
 Professor Marc R. Knight,
 Director,
 Durham Centre for Crop Improvement Technology,
 School of Biological and Biomedical Sciences,
 Durham University,
 South Road,
 Durham DH1 3LE.
 Tel: +44 191 33 41224
 Fax: +44 191 33 41201
 Website: http://www.dur.ac.uk/dccit/
 ***
  
  
  
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Re: [galaxy-user] Zoom function on workflow editor?

[Dannon Baker]

Arthur,

There is no zoom for the main editor window, though you can use(and resize) the 
little mini view in the bottom right corner to move around the workflow 
quickly.  You could also use the browser-level zoom (in Chrome and Firefox, at 
least) to see much more at a time.

-Dannon



On Oct 20, 2011, at 10:26 AM, Arthur Goldberg wrote:

 Hi 
 
 Galaxy's cool!
 Is there a zoom function on the workflow editor? (I know about hiding nodes 
 from the tutorial.)
 
 Thanks
 Arthur
 
 -- 
 Senior Research Scientist
 Computational Biology
 Memorial Sloan-Kettering Cancer Center
 cBio Cancer Genomics Portal
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Re: [galaxy-user] Adding new tools in Galaxy

[Dannon Baker]

Makais, 

Any type of command line tool, whether script or a binary executable, can be 
used by Galaxy as long as it's properly installed on the system and accessible 
to the Galaxy user.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
 for more details on how you might call a compiled executable.

Thanks for using Galaxy,

-Dannon

On Oct 6, 2011, at 7:44 AM, Makis Ladoukakis wrote:

 Dear Galaxy developers,
 
 Currently I am adding new tools to my galaxy instance as scripts written in 
 Perl language. I was wandering if there is a way to add tools either as .bin 
 or .exe format or if only scripts are supported. I couldn't find anything 
 about it in the wiki or in the FAQ. 
 
 Thank you,
 Makis Ladoukakis
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Re: [galaxy-user] Adding new tools in Galaxy

[Dannon Baker]

Makais, 

Any type of command line tool, whether script or a binary executable, can be 
used by Galaxy as long as it's properly installed on the system and accessible 
to the Galaxy user.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
 for more details on how you might call a compiled executable.

Thanks for using Galaxy,

-Dannon

On Oct 6, 2011, at 7:44 AM, Makis Ladoukakis wrote:

 Dear Galaxy developers,
 
 Currently I am adding new tools to my galaxy instance as scripts written in 
 Perl language. I was wandering if there is a way to add tools either as .bin 
 or .exe format or if only scripts are supported. I couldn't find anything 
 about it in the wiki or in the FAQ. 
 
 Thank you,
 Makis Ladoukakis
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Re: [galaxy-user] line estimation for pileup generation

[Dannon Baker]

 === Please use Reply All when responding to this email! ===

As a first step, please confirm an exact line count for the files.  See the 
Line/Word/Character count tool in the Text Manipulation section to do this.  
If the estimate is significantly off, please share the history with me and I'll 
take a look to see what happened with those particular datasets.

Thanks!

-Dannon

On Aug 25, 2011, at 6:08 PM, Austin Paul wrote:

 === Please use Reply All when responding to this email! ===
 
 Hello,
 
 I am curious if the line estimation shown in the history window for pileup 
 generation is at all accurate.  I am using the pileup files to generate 
 expression data from bwa mapping for looking at differential expression, but 
 I am having some trouble understanding the line estimates.  For example, for 
 one pileup file, when I cut the reference id column and the number of hits 
 column (columns 1 and 4), the number of lines in the cut file is about 25% 
 that of the pileup file, and for another file it will be 5000%.   How can the 
 number of lines grow 50x when I am just cutting columns from the file?  
 Shouldnt the line estimate be the same? 
 
 Thanks,
 Austin
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Re: [galaxy-user] Move data between histories?

[Dannon Baker]

Yes, you can copy datasets to other histories, no need to re-upload.  To do 
this, click on Options in the history panel, and then Copy Datasets.  From 
here, you can pick a source history (defaulted to the current active history), 
select the datasets to be copied, and then choose a destination history (new or 
existing).

-Dannon

On Apr 28, 2011, at 12:04 PM, Sam White wrote:

 Hi,
 
 I was wondering if there was a way to easily use (or move) data between 
 different histories.  I have a large fasta file that I'd like to use in a 
 work flow, but this fasta file only shows up when I have the original history 
 open.  Is there a way to select data files that exist in different histories 
 or do I have to download the file and re-up it to any new histories that I'd 
 like to use it in?
 
 Thanks in advance for any help.
 
 Sam White
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Re: [galaxy-user] is galaxy down?

[Dannon Baker]

Keith,

We're currently experiencing a small issue with the main galaxy server.  If you 
could wait a while and then retry, it should be fully functional again soon.

-Dannon

On Mar 25, 2011, at 11:01 AM, Keith E. Giles wrote:

 I keep getting a SERVER ERROR message.  Is galaxy down, or is this on my 
 end?
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Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

[Dannon Baker]

Karl,

For the URL you're pasting, is it the full path to a file in your s3 bucket, 
including the protocol (http://) ?  For galaxy to recognize that it needs to 
pull from a URL rather than the contents of the box, you need to use the full 
string.

-Dannon

On Mar 14, 2011, at 4:40 PM, karlerh...@berkeley.edu wrote:

 
 Hello,
 
 I have been able to get Galaxy to instantiate on our Cloud account, and
 would like to use the NGS tools to trim and map Illumina libraries.
 
 However, when I tried to import .txt files (the data contained in these
 files are in fastq format) located in an S3 bucket, Galaxy did not
 recognize them as fastq data.  I tried to import the files via the URL of
 the S3 bucket, and Galaxy just imported the actual name of the URL rather
 than the file itself.
 
 Do I need to change the extension of these .txt files to .fastq?  Or have
 I gotten something wrong with respect to the location of the data in the
 S3 bucket?
 
 thanks for any help!
 
 karl
 
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