We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations:
* No indication of new jobs in paster.log file
* database/pbs script didn't contain any associated job scripts
* in backend database - job table contained their galaxy job id but no command_line input was recorded
Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful.
I am going to send your question over to the galaxy-dev(a)bx.psu.edu
mailing list so that the development community can offer feedback.
Th galaxy-user list is primarily for tool/data usage on the Galaxy
-------- Original Message --------
Subject: [galaxy-user] R scripts for DESeq
Date: Tue, 21 Feb 2012 23:25:35 -0500
From: Liusong Yang <liusongyang2009(a)gmail.com>
I am planning to put DESeq into galaxy. I am a newcomer for both
Galaxy and R. I have already read all of the related discussion in
this group. I also noticed that there are r_wrapper.sh and DESeq.xml
added into galaxy recently under the path of tools.
These lines are from r_wrapper.sh.
### Run R providing the R script in $1 as standard input and passing
### the remaining arguments on the command line
I guess this means we need to give the DESeq R script to the wrapper
as standard input. My question is where or what is the DESeq R
scripts? I installed R and DESeq package, but I can not fund anything
like DESeq.R or something similar? I feel so confusing now. Any
comments or suggestions would be absolutely appreciated!
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We are going to migrate to a new instance of the galaxy server. Our current
instance contains a number of workflows and other data that we would like
to have available on the new server. Is there a way to backup the workflows
and then reload them on the new server?
-Robert Paul Chase
I am trying to set up MACS tool on local Galaxy. Galaxy comes with
it's macs-wrapper.py and macs-wrapper.xml, but it wants to use "macs"
not "macs14" executable.
I tried to to editing macs-wrapper.py to make it use "macs14" instead,
but some options are not the same between the two, and the tool
I would appreciate if someone could give me an advice on where I can
get "macs" executable for 64-bit Linux.
Sergei (Siarhei Manakou) Manakov
California Institute of Technology
+1 626 395 3593
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job ID User Last Update Tool State Command Line Job Runner PID/Cluster ID
2352 xxxx 21 hours ago upload1 upload None None None
2339 yyyy 19 hours ago upload1 upload None None None
The job numbers are consecutive (2339 to 2352) and reflect a problem
for a couple of hours yesterday morning. I believe this was due to the
underlying file system being unmounted (without restarting Galaxy),
and at the time restarting Galaxy fixed uploading files. Test jobs
since then have completed normally - but these zombie jobs remain.
Using the "Stop jobs" option does not clear these dead upload jobs.
Restarting the Galaxy server does not clear them either.
This is our production server and was running galaxy-dist, changeset
5743:720455407d1c - which I have now updated to the current release,
6621:26920e20157f - which makes no difference to these stalled jobs.
Does anyone have any insight into what might be wrong, and how to get
rid of these zombie tasks?
I would like to get some idea about 'database_engine_option_pool_size' and 'database_engine_option_max_overflow' settings. We seem to hit both of these limits whenever a user runs a large workflow with following error:
TimeoutError: QueuePool limit of size 40 overflow 50 reached, connection timed out, timeout 30
These limits are not reached for regular (non-workflow) galaxy jobs. Any help on optimum values for these settings or performance tuning for workflow runs would be appreciated.
Version Info: CentOS 5.7, PostgreSQL 8.4.9, Python 2.6.6, Galaxy revision 26920e20157f.
I seem to have some problems with the visibility of tool outputs in my
workflows. When I flag any given output as visible, Galaxy sometimes
decides to hide it in the resulting history anyway. I can't find any
systematic behavior though. It seems to be rather arbitrary weather
Galaxy decides that the file should be hidden or not. I would estimate
the random hiding to occur on about 50% of my outputs.
Has anyone seen this before?
Frank Sørensen, B.Sc., Programmer
Molecular Diagnostic Laboratory (MDL)
Molekylær Medicinsk Afdeling (MOMA)
Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N
Tlf. +45 7845 5363
I would like to download/export my workflows from the Galaxy main to a local install at my institution. When I use the URL method, I get the following error message:
Data at 'http://main.g2.bx.psu.edu/u/muehlsch12/w/imported-tophat---cuffdiff-paire... ' does not appear to be a Galaxy workflow
Message: No JSON object could be decoded: line 1 column 0 (char 0)
When I want to download a workflow to my local machine, I get a server error (Duplicate headers received from server).
The local install does not recognize publicly published workflows, so that step won't work either.
Thanks for your help,
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Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
> Dear Greg,
> Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
> We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
> On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
>> Hello Ira,
>> I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
>> Greg Von Kuster
>> On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
>>> Dear list,
>>> I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category.
>>> Would it be possible to add a category called Proteomics?
I'm running into this error:
"Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), "
When using SAM-to-BAM tool on a locally install Galaxy using a SGE
cluster. I'm using the last version of galaxy-dist. I'm guessing I
have a problem with the configuration for the tmp folder. I have this
# Temporary files are stored in this directory.
new_file_path = /home/cborroto/galaxy_dist/database/tmp
But I don't see this directory being used and from the error looks
like /tmp in the node is used. I wonder if this is the problem, as I
don't know if there is enough space in the local /tmp directory at the
nodes? I ran the same tool in a subset of the same SAM file and it ran
Also, I see this in the description of the tool:
"This tool uses the SAMTools toolkit to produce an indexed BAM file
based on a sorted input SAM file."
But what I actually need is to sort a SAM file output from bwa, I
haven't found any other way than to converting it to BAM. Looking at
"sam_to_bam.py" I see the BAM file will also be sorted. Would it be
wrong to feed an unsorted SAM file into this tool?
Finally, just to be sure there is nothing wrong with the initial SAM
file, I ran "samtools view ..." and "samtools sort ..." on this file
manually outside of Galaxy and it ran fine.
Thanks in advance,