galaxy-user September 2013

galaxy-user@lists.galaxyproject.org

60 participants
68 discussions

Zooming in and out in Circster
by Ian Donaldson 09 Sep '13

09 Sep '13

Sorry if I am missing some instructions somewhere, but how do you zoom out of a Circster plot? I have zoomed in by double clicking, but cannot work out how to zoom back out? Thanks, Ian

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Re: [galaxy-user] Bam QC and coverage
by Joachim Jacob | VIB | 06 Sep '13

06 Sep '13

Hi Shamsher, Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README). Cheers, Joachim > On 09/04/2013 09:59 PM, shamsher jagat wrote: > I am looking for a tool to perform QC of Bam file especially following > functions: > 1. BAsic information and stat. > 2. Coverage across reference features- gene/ transcripts. > Is it possible to do it in Galaxy? > Thanks -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Re: [galaxy-user] For constructing workflow of workflows
by Jennifer Jackson 06 Sep '13

06 Sep '13

Hi Deblina, The way to track progress is to watch the Trello card. It is always difficult to give reliable estimates with projects still in progress, but I can let you know that this is an important development area for us and it has priority. Take care, Jen Galaxy team On 9/5/13 2:46 PM, patra wrote: > Hi Jen, > > Thanks a lot for your reply and letting me know that the > concept is in progress as of now. Can you please let me know how much > time approximately it can take to implement the concept of the "nested > workflows" into galaxy? > > Best Regards, > Deblina. -- Jennifer Hillman-Jackson http://galaxyproject.org

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version_command tag problem
by Wolfgang Maier 05 Sep '13

05 Sep '13

Hi everybody, I'm trying to add the version_command tag to my tools' xml files, but I run into a problem here. Currently I have: <version_command interpreter="python3">aln.py --version</version_command> in my xml. When I run the tool Galaxy tells me that it executed this: python3 /home/me/galaxy-dist/tools/modmapmin/aln.py --version &> /home/me/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1035 but when I check that temporary file it's empty (and so is the tool version line at the end of the run). This is puzzling because when I run that exact command line from my terminal, it writes 0.8.2 to the file just as it should. Any ideas what goes wrong here? Thanks and best wishes, Wolfgang

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NoClassDefFoundError in Picard Paired Read Mate Fixer
by Nicolas Quizon 05 Sep '13

05 Sep '13

Dear Galaxy Gurus, I am a student and still new to Galaxy. I am encountering an error when trying to run the Picard Paired Read Mate Fixer with default settings on Galaxy. The code only runs for a few seconds before failing and displaying the error message. ## exit code=1; stdout= [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; Picard version: 1.91() [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=378470400 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" java.lang.NoClassDefFoundError: org/itadaki/bzip2/BZip2InputStream at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76) Caused by: java.lang.ClassNotFoundException: org.itadaki.bzip2.BZip2InputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 4 more For input I am using data that I have successfully mapped with BWA for Illumina. I currently have Python version 2.7.3 and Java version 1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS. Any help is greatly appreciated! Thanks!

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Bam QC and coverage
by shamsher jagat 05 Sep '13

05 Sep '13

I am looking for a tool to perform QC of Bam file especially following functions: 1. BAsic information and stat. 2. Coverage across reference features- gene/ transcripts. Is it possible to do it in Galaxy? Thanks

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For constructing workflow of workflows
by patra 05 Sep '13

05 Sep '13

Hi, This is Deblina. I am working as a PhD student in Martin Luther University Wittenberg, Halle, Germany. For a project I want to use Galaxy. I need to construct a master workflow with sub-workflows connected to each other. Is it possible to construct "workflows of workflows" in galaxy? Best Regards, Deblina.

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Fwd: About empty no peek problem
by XiaoTao Jiang 03 Sep '13

03 Sep '13

---------- Forwarded message ---------- From: XiaoTao Jiang <biofuture.jiang(a)gmail.com> Date: 2013/9/2 Subject: About empty no peek problem To: galaxy-user-request(a)lists.bx.psu.edu Dear all Today I embed one of my R script into local galaxy, I have encountered a strange problem. The script can successfully in local. However, when I run it online in galaxy, the output file is empty and in history panel, it display empty and no peek. I searched the mailing list, but still can not find solutions to solve it. The command display in sever is : *key part * galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,297 *executing:* R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,493 *execution finished: * R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r galaxy.jobs DEBUG 2013-09-02 17:29:49,538 Tool did not define exit code or stdio handling; checking stderr for success galaxy.tools DEBUG 2013-09-02 17:29:49,697 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/job_working_directory/000/71/galaxy.json' galaxy.jobs DEBUG 2013-09-02 17:29:49,759 job 71 ended I check the generated output file /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat It is empty zero in size and then I run the command in local command R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r The output is correct. Any suggestions will be appreciated !! Xiaotao JIANG Regards, The University of HongKong Department of Civil Engineering

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galaxy-user September 2013