If you need to use PBS Pro with Galaxy 16.01.
by SAPET, Frederic
Hello
Using the previous version of Galaxy (before the 16.01) we were able to use PBS Pro as job management system.
It was ok using PBS (/opt/pbs/12.2.4.142262) and DRMAA (pbs-drmaa-1.0.17).
This only thing to do was to truncate the job name that Galaxy send to PBS.
Indeed, in the file lib/galaxy/jobs/runners/__init__.py you need to add :
self.job_name = self.job_name[:15]
in the AsynchronousJobState class otherwise PBS will reject the job.
Using the current version of Galaxy, this is not enough.
You will need to change another file : lib/galaxy/jobs/runners/drmaa.py
And change jt.jobName = ajs.job_name to jt.jobName = ajs.job_name[:15] in the DRMAAJobRunner class (around line 140)
You will then avoid this error :
galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,880 (18) drmaa.Session.runJob() failed unconditionally
Traceback (most recent call last):
File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/runners/drmaa.py", line 181, in queue_job
external_job_id = self.ds.runJob(jt)
File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/session.py", line 314, in runJob
c(drmaa_run_job, jid, sizeof(jid), jobTemplate)
File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/helpers.py", line 299, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages/drmaa/errors.py", line 151, in error_check
raise _ERRORS[code - 1](error_string)
InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value
galaxy.jobs.runners.drmaa ERROR 2016-03-24 15:23:23,883 (18) All attempts to submit job failed
I hope this will help if you plan to use Galaxy over PBS Pro. We currently used PBS 12.2.4.142262, DRMAA 1.0.19 and the latest galaxy (after a git pull command)
Fred
---
Frederic Sapet
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
CS 90126
63720 CHAPPES
FRANCE
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>
5 years, 8 months
Request help to configure local galaxy in Git
by Manonanthini Shanmuganathan
Hi Galaxy Developer,
I have been trying to install Galaxy in my windows system using git.I
have tried using cygwin also.I have been trying for this since March
2nd , I am getting this error,
"ManoNathan@Mano MINGW64 ~/galaxy ((v16.01))
$ sh run.sh
Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.
tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1679k 100 1679k 0 0 357k 0 0:00:04 0:00:04 --:--:-- 447k
Verifying /tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz
checksum is aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc
Traceback (most recent call last):
File "<string>", line 1, in <module>
IOError: [Errno 2] No such file or directory:
'/tmp/galaxy-virtualenv-GUksti/virtualenv-13.1.2.tar.gz'
"
So I am unable to run galaxy in my system.Please help me in this regard.
I have installed XAMPP(for mysql and apache server) in my system(Windows 10).
Thanks and Regards,
Manonanthini Thangam
PhD Scholar,
Bioinformatics Lab,
AU-KBC Research Centre,
MIT Campus,Anna University,
Chromepet,Chennai.
5 years, 8 months
Troubleshooting BAM file upload issues
by Amelia Ireland
I'm setting up a Galaxy instance on a new server and am having some issues
with BAM file uploads. I'm using the BAM files supplied with JBrowse for
testing purposes. I have Galaxy installed on my laptop and file uploads are
working fine, so it's evidently an issue with the server and/or OS
configuration.
Attempting to upload a BAM file returns the message
"The uploaded binary file contains inappropriate content"
and the upload is empty.
The server is running Scientific Linux and uses the Environment Modules
system for dependency management. I can successfully upload bed and bigwig
files, which suggests that samtools is being loaded and functioning
correctly.
If someone can suggest some troubleshooting steps, I would be most grateful.
Thanks!
Amelia
Integrated Microbial Genomics (IMG)
JGI / LBL
5 years, 8 months
package_bowtie_2_2_6 error
by changyu_fan
Hello All,
We try to install bowtie2 package in galaxy but failed.
Tool shed: toolshed.g2.bx.psu.edu
Name: package_bowtie_2_2_6
Owner: iuc
Here is the message:
tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract
os.chmod( absolute_filepath, unix_permissions )
*"[Errno 2] No such file or directory:
'./database/tmp/tmp-toolshed-mtdpzqr7H/bowtie2-2.2.6/bowtie2-2.2.6/'"*
Any help will be appreciated.
Thanks
Changyu
5 years, 8 months
Re: [galaxy-dev] perl version 5.18.1 repository error
by Rathert, Philipp, Dr.
Dear Nicola,
now it looks like package_gnu_coreutils_8_22
is generating an error
gnu_coreutils <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?r...> 8.22 package Error Shutting down process id 23231 because it generated no output for the defined timeout period of 3600.0 seconds.
I didn't find anything an this error on the web and I am not sure how I can fix this...
cheers,
philipp
-----Original message-----
From: Nicola Soranzo <nsoranzo(a)tiscali.it>
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] perl version 5.18.1 repository error
Hi Philipp,
can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it.
Cheers,
Nicola
On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
Dear all,
i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.
however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies:
Tool shed repository:package_perl_xml_parser_expat_2_41
Tool shed repository changeset revision:1ce3818a8eb9
Tool dependency status:Error
Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc.
Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9
Is this an error of my local instance or is the revision missing on the toolshed?
Thank you very much for your help.
Cheers,
philipp
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5 years, 8 months
Python 2.7 vs 2.6 for galaxy after 16.01
by D K
Hi Galaxy Devs,
This may be premature but I read that for Galaxy after 16.01 that the plan
is for python 2.6 to no longer be supported. I'm currently running CentOS
6.6 which uses python 2.6. In order to be able to use newer versions of
Galaxy is my only option to upgrade to a newer version of CentOS? Is it
possible to use Conda, RedHat Software Collections or some other similar
method instead of doing this upgrade?
Thanks!
5 years, 8 months
Data set too large
by Tiara Smith
Hell I am accessing galaxy from a main computer on my university campus. I
am having difficulty uploading my exome files and keep getting the
following error prompt:
ndex30_CACCGG_L001-L002_R1_001.bam
*2.8* GB
Auto-detect
----- Additional Species Are Below -----
*Failed: *File exceeds 2GB. Please use a FTP client.
Is there a way to increase my file upload limit? my data sets range from
1.9GB ro 3.9GB.
thank you for your help.
Tiara Smith
5 years, 8 months
automatic adding of a tab in a fastq header
by Fabien Mareuil
Hi,
We got a problem with the new version of Data libraries. When we upload
a fastq file from a User Directory, a tabulation character is added in
the header in replacement of a space character.
from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
This behavior causes an error with cutadapt 1.6 (maybe with other tools)
because it doesn't work with tab character. With the direct upload tool
or the deprecated version of Data Libraries no tab character is added.Do
you have some idea to correct this problem? Thanks a lot Best regards --
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mareuil(a)pasteur.fr <mailto:fabien.mareuil@pasteur.fr> | Institut
Pasteur 25,28 rue du Docteur Roux 75015 Paris, France
5 years, 8 months
perl version 5.18.1 repository error
by Rathert, Philipp, Dr.
Dear all,
i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.
however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies:
Tool shed repository:package_perl_xml_parser_expat_2_41
Tool shed repository changeset revision:1ce3818a8eb9
Tool dependency status:Error
Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc.
Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9
Is this an error of my local instance or is the revision missing on the toolshed?
Thank you very much for your help.
Cheers,
philipp
5 years, 8 months
