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
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
On 9/12/13 10:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin mathieu.ba...@irisa.fr
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
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
It might be due to this bug:http://dev.list.galaxyproject.org/Limit-number-of-Jobs-to-Trinity-tt4661790.html#a4661874
Ilya
From: Ganote, Carrie L cgan...@iu.edu
Date: Monday, October 7, 2013 1:46 PM
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev]
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
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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
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
Thanks for getting this fixed so quickly!
Ilya
On 5/2/13 4:32 PM, Dave Bouvier d...@bx.psu.edu 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 13:01:54.000, Sytchev, Ilya wrote
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 idj...@gmail.com wrote:
I was pretty much interested in Bio-Linux. However, the
JSONDecodeError will be raised if the given JSON document is not valid.
http://simplejson.readthedocs.org/en/latest/
Ilya
From: Rob Leclerc robert.lecl...@gmail.com
Date: Friday, March 8, 2013 12:01 AM
To: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: [galaxy-dev] BioBlend: Problem
-of-dataset-display/diff
Thanks,
-John
On Thu, Dec 13, 2012 at 2:20 PM, Sytchev, Ilya
isytc...@hsph.harvard.edu wrote:
So, it turns out that it's currently impossible to download datasets
programmatically without using username/password (when require_login is
set to True) because Galaxy API does
2:41 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote:
Hi,
Is it possible to download a dataset when require_login=True in
universe_wsgi.ini using the API key?
Thanks,
Ilya
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Hi,
Is it possible to download a dataset when require_login=True in
universe_wsgi.ini using the API key?
Thanks,
Ilya
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in your mail client. To manage your subscriptions to this
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
is
failing?
Thanks,
JJ
--
Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +
From: Sytchev, Ilya isytc...@hsph.harvard.edu
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] No output from IGVtools tile
Message-ID: ccd9d465.30c7%isytc
The error is gone, thank you very much! What was the problem?
Ilya
On 11/27/12 5:34 PM, Jim Johnson johns...@umn.edu 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 3:18 PM, Sytchev, Ilya wrote
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
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