[galaxy-dev] SLURM timeouts

Hi, I'm running a fork of galaxy-central latest_2014.08.11. The instance is configured to run jobs on a SLURM cluster. The problem is that the SLURM controller sometimes becomes too busy which results in errors like: galaxy.jobs.runners.drmaa INFO 2014-10-23 21:10:47,768 (1813/22896754) job left

Re: [galaxy-dev] Problems with tophat in local instance

Hi, It sounds like the reference genome is not set up for the Tophat tool.  Please have a look at the instructions (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) under "Tools and Their Corresponding loc Files" and "Bowtie and Tophat". Ilya From: Rainy Luo

[galaxy-dev] Stopping jobs by deleting history via API

Hi, I was wondering if there are any near term plans to fix this issue? https://trello.com/c/Tbota8xG/992-deleting-history-using-the-api-does-not-d elete-stop-jobs Thanks, Ilya ___ Please keep all replies on the list by using "reply all"

Re: [galaxy-dev] Stopping jobs by deleting history via API

Could anyone familiar with the code comment on whether addressing this problem would require a lot of work or might there be a quick fix? Thanks, Ilya On 8/15/13 2:36 PM, "Sytchev, Ilya" wrote: >Hi, > >I was wondering if there are any near term plans to fix this issue? &g

Re: [galaxy-dev] Dynamic job runner not being dispatched for a tool

It might be due to this bug: http://dev.list.galaxyproject.org/Limit-number-of-Jobs-to-Trinity-tt4661790.html#a4661874 Ilya From: , Carrie L Date: Monday, October 7, 2013 1:46 PM To: "galaxy-dev@lists.bx.psu.edu" Subject: [galaxy-dev] Dynami

[galaxy-dev] Dealing with cluster job preemption

Hi, Our Galaxy instance is configured to use LSF. The problem is that sometimes our jobs get preempted (stopped and re-queued to let higher-priority jobs run) and Galaxy thinks that those jobs have failed. Is there any way around that by any chance? Thanks, Ilya ___

Re: [galaxy-dev] Jobs deleted staying in 'dr' status

On 9/12/13 10:35 AM, "Peter Cock" wrote: >On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin >wrote: >> Hi all, >> >> We have been developing our own Galaxy instance for a while now. We >>have a >> cluster on which the job are sent to be executed, it is managed through >>SGE. >> Usually, communica

[galaxy-dev] $GALAXY_SLOTS is set incorrectly when using LSF

Hi, I've noticed that $GALAXY_SLOTS that was always set to 1 when using LSF. It turns out that LSF specifies the number of parallel slots using $LSB_DJOB_NUMPROC env variable which isn't checked in lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh. A diff that describes the fix i

[galaxy-dev] No output from IGVtools tile

Hi, I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs. Also, IGVtools tile

Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31

file, and I'll try to find out what is >failing? >Thanks, >JJ > > >> -- >> >> Message: 6 >> Date: Tue, 27 Nov 2012 07:22:30 + >> From: "Sytchev, Ilya" >> To: "galaxy-dev@lists.bx.psu.edu" &g

Re: [galaxy-dev] No output from IGVtools tile

The error is gone, thank you very much! What was the problem? Ilya On 11/27/12 5:34 PM, "Jim Johnson" wrote: >Ilya, >I fixed the igvtools_tile.xml tool config and pushed it to the toolshed. >Thanks for finding and reporting the problem. >JJ > >On 11/27/12

Re: [galaxy-dev] Uploading Files on Local Cluster Install

LimitRequestBody has a max value of 2147483647 (2GB). You probably want to set it to zero to disable the limit: http://httpd.apache.org/docs/current/mod/core.html#limitrequestbody Also, you may be running into memory limits on the server, especially if it's running a 32-bit OS (where each process

[galaxy-dev] Downloading datasets without username/password when login is required

Hi, Is it possible to download a dataset when require_login=True in universe_wsgi.ini using the API key? Thanks, Ilya ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this a

Re: [galaxy-dev] Downloading datasets without username/password when login is required

11/12 2:41 PM, "Sytchev, Ilya" wrote: >Hi, > >Is it possible to download a dataset when require_login=True in >universe_wsgi.ini using the API key? > >Thanks, >Ilya > ___ Please keep all replies on the

Re: [galaxy-dev] Downloading datasets without username/password when login is required

qu >ivalent-of-dataset-display/diff > >Thanks, >-John > >On Thu, Dec 13, 2012 at 2:20 PM, Sytchev, Ilya > wrote: >> So, it turns out that it's currently impossible to download datasets >> programmatically without using username/password (when require_login is >&

Re: [galaxy-dev] BioBlend: Problem Running Example file

JSONDecodeError will be raised if the given JSON document is not valid. http://simplejson.readthedocs.org/en/latest/ Ilya From: Rob Leclerc Date: Friday, March 8, 2013 12:01 AM To: "galaxy-...@bx.psu.edu" Subject: [galaxy-dev] BioBlend: Pr

Re: [galaxy-dev] Teaching using Galaxy

Hi David, These short courses may be of interest: http://scriptogr.am/ohofmann/intro-to-galaxy http://scriptogr.am/ohofmann/rna-seq http://scriptogr.am/ohofmann/exome-seq Ilya On 4/25/13 10:11 AM, "David Joly" wrote: >I was pretty much interested in Bio-Linux. However, the version of Galax

Re: [galaxy-dev] Problem accessing test tool shed repositories

Thanks for getting this fixed so quickly! Ilya On 5/2/13 4:32 PM, "Dave Bouvier" wrote: >Ilya, > >Thank you for reporting this issue, a fix has been committed in >9627:8d8368ab03ff, and the test tool shed has been updated. > >--Dave B. > >On 5/2/13 13:01:

[galaxy-dev] Workflow annotations

Hi, I'm running a local Galaxy instance and using the test tool shed. I've just noticed that workflows imported from the test tool shed don't have either workflow level or tool level annotations available (even though they are present in the .ga file in the repository). On the other hand, if a w

Re: [galaxy-dev] Workflow annotations

Awesome, thanks! What about workflows imported from tool shed repositories? For example, I have two annotated workflows in this repository: http://testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test. When I install them from the repository to my local galaxy-central instance (9722:6d72b2db32c