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

Galaxy & IGV display error
by PROTASIO＠clinic.ub.es 03 Dec '12

03 Dec '12

Hi all, I'm having problems when I click to visualize one BAM file from galaxy to IGV version 2.1.24. I've tried the local and also the web display options but I have the same problem. I have tried also to download first the bam file from galaxy and then loading into IGV manually and it works. I also have tried to modify the .jnlp generated but it does not work. IGV shows the next error message: ERROR [2012-11-26 11:44:54,591] [IGV.java:1555] [pool-1-thread-1] net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available) ERROR [2012-11-26 11:44:54,592] [IGV.java:1494] [pool-1-thread-1] Error loading tracks org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://172.21.104.21:8080/display_application/9e23127bd2c9a880/igv_bam/web_…<br>Premature EOF; BinaryCodec in readmode; streamed file (filename not available) Thanks for your help. Joan Protasio, Bioinformatician & Software Engineer Bioinformatics Platform August Pi i Sunyer Biomedical Research Institute (IDIBAPS) C/ Rosselló 153, Barcelona http://bioinformatics.fcrb.es<http://bioinformatics.fcrb.es/> +34 93 227 54 00 ext. 4522

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Data/history/user export and import
by Bossers, Alex 02 Dec '12

02 Dec '12

Dear all, Would it be possible somehow to not only export a single history of a user (to file) but also all histories of a user in one go. Or even all user-bound histories/settings and such? I would like to import them into another galaxy instance (basically from our internal development (galaxy_central) server to our public production (galaxy-dist) server), but going over them one-by-one will be a laborious task. Both instances are up-to-date. I do have admin access to both the galaxy instances (as we own them) so admin bound tools and/or possibilities from commandline would be suitable as well. Since I am unsure where it fits in the user-list or dev-list I cross-posted to both (sorry). Thanks in advance! Alex

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(no subject)
by Perez, Ricardo 02 Dec '12

02 Dec '12

Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez.

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hardware requirement for galaxy
by Huayan Gao 01 Dec '12

01 Dec '12

Hi there, I'm interested in the specifics of your Penn State setup. Can you send it to me? Thanks, Huayan

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Issue when enabling use_tasked_jobs with torque and nfs
by Carlos Borroto 30 Nov '12

30 Nov '12

Hi, In my environment when I activate 'use_tasked_jobs' I'm getting this message in "Info" with ncbi_blast wrappers: /local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0: Job output not returned from cluster Still the dataset with the blast result is green and contains the expected information. In the log I see: galaxy.jobs.runners.drmaa WARNING 2012-11-30 13:45:32,760 Job output not returned from cluster: [Errno 2] No such file or directory: '/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout' And from torque I get this email: PBS Job Id: 1013.head Job Name: g9_toolshed_g2_bx_psu_edu_repos_devteam_ncbi_blast_plus_ncbi_blastn_wrapper_0_0_14_carlos_borroto_gmail_com Exec host: node01/0 An error has occurred processing your job, see below. Post job file processing error; job 1013.head on host node01/0 Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU Unable to copy file /var/spool/torque/spool/1013.head.ER to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmerr *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmerr': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.ER I think the problem is I'm forcing torque to use my nfs mounted shared file system: # cat /var/spool/torque/mom_priv/config $pbsserver head $usecp *:/home /home $usecp *:/local /local I can confirm this configuration is working fine with any other job not submitted through galaxy, both files are correctly copied to the working dir in that case. I'm using drmaa runner. I tried pbs, but in that case even without enabling tasked_jobs, while the err and out files are correctly copied and everything seems fine as far as I can tell, galaxy complains it can not find them. I tried increasing "retry_job_output_collection", but that didn't help. Cheers, Carlos

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use multiple cores in BWA
by Fenglou Mao 30 Nov '12

30 Nov '12

I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried "Full Parameter List", anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank

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December 2012 Galaxy Update
by Dave Clements 30 Nov '12

30 Nov '12

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Changing interface design
by Philipe Moncuquet 30 Nov '12

30 Nov '12

Hi I am not satisfied with some colors of the interface. I am color blind and it's hard to discriminate between job running (light yellow) and job done (light green). Well most of the time I focus on red jobs right but anyway I would like to be able to change these stuff. Can anybody point me the file I am supposed to modify to be able to do so. Many thanks in advance. Philippe

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Variable output number in workflows
by Pierre Pericard 30 Nov '12

30 Nov '12

Dear all, We've been actively developping xml wrappers for new programs in our instance of Galaxy and we encountered some problems with multiple outputs number while using these tools in a workflow. 1/ In the first case, inputs can be 1 single file or 2 paired files and the program output name is different depending on which case. The input problem is resolved using <conditional> and following http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files we implemented the outputs as such: <outputs> <data name="nameSorted.single.bam" format="bam" from_work_dir="alignReads/alignReads.nameSorted.bam" label="nameSorted single" > <filter>inputs['paired_or_single'] == 'single'</filter> </data> <data name="nameSorted.paired.bam" format="bam" from_work_dir="alignReads/alignReads.nameSorted.PropMapPairsForRSEM.bam" label="nameSorted paired" > <filter>inputs['paired_or_single'] == 'paired'</filter> </data> </outputs> However, when using this tool in a workflow, the toolbox always presents the 2 outputs, whether we choose 1 or 2 inputs. Is there any way to have only one output in the toolbox but from a different file depending on the input ? 2/ the second case is very similar to the one described in http://dev.list.galaxyproject.org/outputting-different-numbers-of-files-bas…. When we input a single file the output is also a single file, and when we input two paired files the program outputs two files. Thanks again to the <conditional> tag the input problem was taken care of, but we would like the workflow toolbox to present 1 or 2 outputs (ideally with all 3 names different) depending on how many files are in the input. Is there any way to do so other than making 2 different versions of the xml or displaying all 3 outputs in the workflow toolbox ? Thanks in advance, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique - CNRS-UPMC Place Georges Teissier, 29680 Roscoff FRANCE http://abims.sb-roscoff.fr/

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Workflow loading problem
by Shaun Webb 30 Nov '12

30 Nov '12

Hi, I have imported a workflow to my local Galaxy with unrecognised tools. When I try to edit this workflow it will not load. I now realise I have the same problem with some existing workflows where a tool has been removed from Galaxy, I would like to replace these workflow steps without creating a new workflow. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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