- galaxy-dev - lists.galaxyproject.org

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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Which version of GATK work with Galaxy?
by Fenglou Mao 30 Nov '12

30 Nov '12

When I use an old version of GATK, it failed with a report "-nt" option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report "-et NO_ET" need a key file to work since new GATK force users to report usage unless we obtain a key file, but it seems no place for galaxy to specify the key file. Any help? Thanks, Frank

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Local Instance permissions.
by Perez, Ricardo 30 Nov '12

30 Nov '12

Hi, We are implementing a local instance of Galaxy and I had a quick question, is it wrong to give Galaxy access to the UCSC databases? Thank you for your time and patience, --Ricardo Perez

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How to Tell if Apache XSendFile is Working Properly
by greg 29 Nov '12

29 Nov '12

I just set up XSendFile on my local Galaxy install by following the instructions here: [1] http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy#Sending_files_usi… However I'm wondering how to verify that uploads are in fact using XSendFile? (Galaxy still seems to create a job after the upload and the job takes a while to run.) Thanks, -Greg

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Uploading Files on Local Cluster Install
by greg 29 Nov '12

29 Nov '12

I just finished setting up a local install on our cluster but I'm having trouble uploading files. I was able to (successfully?) upload one 160MB fasta file. But any further uploads I try, they just hang. Here's the information from the log file: paste.httpserver.ThreadPool INFO 2012-11-28 12:15:18,190 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers galaxy.tools.actions.upload_common INFO 2012-11-28 12:20:36,597 tool upload1 created job id 4 galaxy.jobs.handler INFO 2012-11-28 12:20:38,386 (4) Job dispatched galaxy.jobs.runners.drmaa INFO 2012-11-28 12:20:38,930 (4) queued as 3718641 galaxy.objectstore CRITICAL 2012-11-28 12:21:03,071 /home/galaxy/job_working_directory/000/4 delete error [Errno 39] Directory not empty: '/home/galaxy/job_working_directory/000/4' paste.httpserver.ThreadPool INFO 2012-11-28 12:21:55,763 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:28:26,466 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:35:09,662 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers paste.httpserver.ThreadPool INFO 2012-11-28 12:46:35,565 kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting) ave time N/A, max time 0.00sec, killed 0 workers The first upload that worked was around 12:20 (above), and the second failed one was at 12:40. The log file doesn't seem to even mention it? Could that error have killed the server somehow? Let me know if I can provide more info. Thanks, Greg

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file descriptors bug
by Fabien Mareuil 29 Nov '12

29 Nov '12

Hello We found a problem when we execute a job in local mode with galaxy. When a job is running and galaxy restarted, we obtain this error : message: socket.error: [Errno 98] Address already in use All the file descriptors are passed from parent to child by default with subprocess.popen. If you want to close all file descriptors excepted stdin, stdout and stderr, you have to use the option: close_fds = True. In local.py line 84-90: proc = subprocess.Popen( args = command_line, shell = True, cwd = job_wrapper.working_directory, stdout = stdout_file, stderr = stderr_file, env = os.environ, preexec_fn = os.setpgrp, close_fds = True ) I hope this will help resolving this bug Thank you in advance. Sincerely Fabien Mareuil -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

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Stitch Gene blocks return empty result???
by 张坤山 29 Nov '12

29 Nov '12

Hi all, I trying to stitch some MAF from bed12 file using "Stitch Gene blocks". Galaxy successfully recognized my BED file and finished stitch, but no sequence in the result. My BED file is like: chr1 14662810 14707010 TCONS_00007949 0 - 14707010 14707010 0 5 229,139,106,162,77, 0,4387,4975,8271,44123, chr1 84928679 84942052 TCONS_00027714 0 + 84942052 84942052 0 4 64,173,111,398, 0,1330,12292,12975, chr1 91200237 91254779 TCONS_00030473 0 - 91254779 91254779 0 3 285,177,104, 0,52636,54438, I choose 36 mammals to stitch blocks. Galaxy gives me result like: >mm9.TCONS_00007949 >hg19.TCONS_00007949 >panTro2.TCONS_00007949 No sequence in result.What happen?? Kunshan

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