November 2012 - galaxy-dev - lists.galaxyproject.org

Error running SICER peak caller
by pjt2＠alumni.ubc.ca 27 Nov '12

27 Nov '12

Hi, I am trying to run SICER (version 0.0.1) in galaxy to call peaks using the galaxy interface browser. My workflow is as follows. First I uploaded BAM files of my ChIP tag and input tag data, I then convert these to SAM files with the SAMtools tool, and then convert the SAM files to intervals using the SAM to interval tool. Finally I convert the interval files to BED6 format using the convert format tab in the attributes of each file. At every step the tools work successfully. Finally I go to run SICER on the ChIP tag and input BED6 files I've made but after starting successfully I shortly get the following error: "An error occurred running this job: Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/peak_calling/sicer_wrapper.py", line 156, in if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/peak_calling/sicer_wrapper.py", li" This is all I can see of the error message. I've tried several times now but it still gives the same error. Am I doing something wrong? How do I get SICER to work in galaxy? Thanks, Peter Thompson, PhD Candidate Department of Medical Genetics Life Sciences Centre, UBC Vancouver, BC CANADA V6T 1Z3

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Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31
by Jim Johnson 27 Nov '12

27 Nov '12

Ilya, Could you send me a failing input file, and I'll try to find out what is failing? Thanks, JJ > ------------------------------ > > Message: 6 > Date: Tue, 27 Nov 2012 07:22:30 +0000 > From: "Sytchev, Ilya" <isytchev(a)hsph.harvard.edu> > To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> > Subject: [galaxy-dev] No output from IGVtools tile > Message-ID: <CCD9D465.30C7%isytchev(a)hsph.harvard.edu> > Content-Type: text/plain; charset="us-ascii" > > 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 tool runs successfully by itself from the command line > on the same input WIG file from the same user account that runs this > Galaxy instance. > > Standard out and error from running tile in Galaxy are below. I was > wondering if anyone had a similar problem with IGVtools in their Galaxy > instance. > > Thanks, > Ilya > > > stdout: > > Tile. File = input_file.wig > Max zoom = 7 > Probe file = None > Window functions: mean > IGV directory: /n/galaxy/home/galaxy_scc/igv > INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome > loaded > > Processing chromosome chr19 > .........10.0% > .........20.0% > .........30.0% > .........40.0% > .........50.0% > ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring > data from non-existent locus. Probe = null Locus = > chr19:61342442-61342477. chr19 length = 61342430 > Group idx: 1 > 100.0% > > > > stderr: > > cp: cannot stat > `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/jo > b_working_directory/000/100/output.tdf': No such file or directory > >

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DRMAA job will now be errored -> Segmentation fault
by Peter Cock 27 Nov '12

27 Nov '12

Hi all, Something has changed in the job handling, and in a bad way. On my development machine submitting jobs to the cluster didn't seem to be working anymore (never sent to SGE). I killed Galaxy and restarted: Starting server in PID 12180. serving on http://127.0.0.1:8081 galaxy.jobs.runners.drmaa ERROR 2012-11-15 09:56:28,192 (320/None) Unable to check job status Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 296, in check_watched_items state = self.ds.jobStatus( job_id ) File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 522, in jobStatus _h.c(_w.drmaa_job_ps, jobName, _ct.byref(status)) File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) InvalidArgumentException: code 4: Job id, "None", is not a valid job id galaxy.jobs.runners.drmaa WARNING 2012-11-15 09:56:28,193 (320/None) job will now be errored ./run.sh: line 86: 12180 Segmentation fault (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@ I restarted and it happened again, third time lucky. I presume this was one segmentation fault for each orphaned/zombie job (since I'd tried two cluster jobs which got stuck). I was running with revision 340438c62171, https://bitbucket.org/galaxy/galaxy-central/changeset/340438c62171578078323… as merged into my tools branch, https://bitbucket.org/peterjc/galaxy-central/changeset/d49200df0707579f41fc… Any thoughts? Thanks, Peter

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multithreaded tools
by Andreas Kuntzagk 27 Nov '12

27 Nov '12

Hi, I'm wandering how galaxy supports tools that are multithreaded or multi-process. When working with lastz I noticed that it starts 4 parallel processes. Is that always so? Can this be adjusted? What other tools also are multi-process? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Can't get automatic toolshed installation to work....
by Nikhil Joshi 27 Nov '12

27 Nov '12

Hi all, We just upgraded our local galaxy to the latest version and now I am trying to get automatic tool installation to work properly. I changed the universe_wsgi.ini file to enable the toolshed xml file, I created a "shed_tools" directory one above the galaxy install, and restarted galaxy. But when I try to install a repository, I get this error as a popup: "Initializing repository installation failed". I tried this with various repositories, but I get the same error. Then when I go to "Manage installed tool shed repositories", all of the repositories I tried to install are stuck in the "Cloning" state. Finally, if I try to uninstall any of them, I get this error, with a traceback: AttributeError: 'NoneType' object has no attribute 'startswith' Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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lastz on local galaxy failing
by Andreas Kuntzagk 27 Nov '12

27 Nov '12

Hi, when I start a lastz job it submits a job to GridEngine. But this job seems to hang. The process running is python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source= ... This wrapper seems to not start a lastz but lastz is in the path. After 2 days then Galaxy shows "Job did not produce output" Here is the paster.log from the start of the job. galaxy.jobs DEBUG 2012-11-15 09:03:07,539 (254) Working directory for job is: /data/galaxy/galaxy-dist/database/job_working_directory/000/254 galaxy.jobs.handler DEBUG 2012-11-15 09:03:07,540 dispatching job 254 to drmaa runner galaxy.jobs.handler INFO 2012-11-15 09:03:07,688 (254) Job dispatched galaxy.tools DEBUG 2012-11-15 09:03:07,980 Building dependency shell command for dependency 'lastz' galaxy.tools WARNING 2012-11-15 09:03:07,981 Failed to resolve dependency on 'lastz', ignoring galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,669 (254) submitting file /data/galaxy/galaxy-dist/database/pbs/galaxy_254.sh galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,670 (254) command is: python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source=cached --source_select=pre_set --out_format=sam --input2=/data/galaxy/galaxy-dist/database/files/027/dataset_27795.dat --input1="/data/galaxy/galaxy-dist/tool-data/shared/ucsc/hg18/seq/hg18.2bit" --ref_sequences="None" --pre_set_options=yasra98 --identity_min=0 --identity_max=100 --coverage=0 --output=/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat --unmask=yes --lastzSeqsFileDir=/data/galaxy/galaxy-dist/tool-data; cd /data/galaxy/galaxy-dist; /data/galaxy/galaxy-dist/set_metadata.sh ./database/files /data/galaxy/galaxy-dist/database/job_working_directory/000/254 . /data/galaxy/galaxy-dist/universe_wsgi.ini /data/galaxy/galaxy-dist/database/tmp/tmpL4MMJV /data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy.json /data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_in_HistoryDatasetAssociation_288_9ynzEN,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_kwds_HistoryDatasetAssociation_288_AEIseO,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_out_HistoryDatasetAssociation_288_RhsufT,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_results_HistoryDatasetAssociation_288_86DYsR,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_override_HistoryDatasetAssociation_288_HMRNEG galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,676 run as user ['kuntzagk', '600'] galaxy.jobs DEBUG 2012-11-15 09:03:08,676 (254) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /data/galaxy/galaxy-dist/database/job_working_directory/000/254 kuntzagk 600 galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:09,148 (254) Job script for external submission is: /data/galaxy/galaxy-dist/database/pbs/254.jt_json 141.80.188.178 - - [15/Nov/2012:09:03:10 +0200] "POST /galaxy/root/history_item_updates HTTP/1.1" 200 - "http://bbc.mdc-berlin.de/galaxy/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0" galaxy.jobs.runners.drmaa INFO 2012-11-15 09:03:11,553 (254) queued as 1282605 galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:11,767 (254/1282605) state change: job is running -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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How to delete a toolshed tool completely or change category
by Andreas Kuntzagk 27 Nov '12

27 Nov '12

Hi, In the past I installed bwa_wrapper from the toolshed. Unfortunately I must have choosen a wrong category. Currently it is not part of any tool section. According to integrated_tool_panel.xml it's supposed to be part of this section: <section id="ngs:_assembly" name="NGS: Assembly" version=""> while it contains another section with the same name and a different id: <section id="ngs_assembly" name="NGS: Assembly" version=""> I tried to rectify this by deleting and reinstalling but unfortunately there is no way to really reinstall and it always ends up with the same problem again. Is there a way to really uninstall? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Occasionally, commandline tools are not found
by Joachim Jacob 27 Nov '12

27 Nov '12

Hi all, This is a strange error, still lingering around on our Galaxy. From time to time, some tools fail, with the same error: job stderr: /bin/sh: fastx_clipper: command not found So I log in as the user Galaxy, and run the tools successfully on the commandline. The solution is to restart the complete machine. I run CentOS6.3 with Galaxy distro 12fcd068b12e (Okt 23 release). Apparently, the PATH of the Galaxy session gets corrupted during running Galaxy, and I don't know where or how. Anybody a hint? Perhaps somebody knows how to reset the PATH of the current sessions where Galaxy is running as? Thanks, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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No output from IGVtools tile
by Sytchev, Ilya 27 Nov '12

27 Nov '12

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 tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance. Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance. Thanks, Ilya stdout: Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded Processing chromosome chr19 .........10.0% .........20.0% .........30.0% .........40.0% .........50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0% stderr: cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/jo b_working_directory/000/100/output.tdf': No such file or directory

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how to get annotation files for rna-seq
by Dr. Mira A. Bisso 26 Nov '12

26 Nov '12

Dear help; How to get the human annotation file for RNAseq analysis, for mapping by BWA and for RNAseq analysis, on Cufflinks and cuffdiff tools on galaxy? Mira Thanks [image001] Mira Bosso, M.Sc, B.D.S Research associate Pancreatic Islet Biology and Transplantation Unit P.O.Box 1180, Dasman 15462, Kuwait Phone: +965 2224 2999 Ext.2803 Mob: +96599500197 Email: mira.bisso(a)dasmaninstitute.org<mailto:mira.bisso@dasmaninstitute.org>

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