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

Is there a way to turn of the pretty display for VCF files
by Anthonius deBoer 29 May '12

29 May '12

Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon

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starting galaxy server - Paste/egg installation
by Shantanu Pavgi 29 May '12

29 May '12

Hi, Has there been any change in the way galaxy-dist server is started up? I am getting following error after running 'run.sh --daemon' command after galaxy initializes config files from .sample files: {{{ Initializing community_wsgi.ini from community_wsgi.ini.sample Initializing datatypes_conf.xml from datatypes_conf.xml.sample … ... Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Command 'serve' not known (you may need to run setup.py egg_info) No commands registered. Have you installed Paste Script? (try running python setup.py develop) }}} Do I need to install eggs separately using some other script? Any help? -- Shantanu

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Unable to Load Any History From File
by Todd Oakley 29 May '12

29 May '12

Hello, I want to be able to analyze data on one Galaxy instance, and store histories more permanently on another. This is critical for us as we have storage usage limits on the shared machine with the most computational power. Although I am now able to export histories as a file, I cannot import histories. When I choose under history "Import From File", I get a message saying the history is importing and will be visible when finished. However, I never see the history. I've tried many combinations with different histories - saving and downloading in the same Galaxy instance, downloading on one instance and importing on the other, saving the file in a different location altogether or using the link provided in export history. I've not been able to import a history from a file. Thanks for any advice. Todd -- *************************************** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA ***************************************

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Uncaught exception when submitting jobs
by Anthonius deBoer 29 May '12

29 May '12

Hi, All of a sudden I am getting these errors when I submit a job in my Galaxy system. I can't recall I changed anything and I checked the universe file but nothing obvious there... Any ideas? Thanks Thon galaxy.jobs.runners.drmaa ERROR 2012-05-29 09:40:46,873 Uncaught exception queueing job Traceback (most recent call last): File "/home/tdeboer/code/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 133, in run_next self.queue_job( obj ) File "/home/tdeboer/code/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 213, in queue_job job_id = self.ds.runJob(jt) File "/home/tdeboer/code/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/home/tdeboer/code/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 "/home/tdeboer/code/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)) DeniedByDrmException: code 17: ERROR! invalid option argument "----"

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Galaxy
by Twaha Mlwilo 29 May '12

29 May '12

Hello all, I would like to learn Galaxy and more, as my interest is in Bioinformatics and computational research.Please any help for tutorial materials Thank you in advance Twaha

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Batch limit on Wokflows
by Petit III, Robert A. 29 May '12

29 May '12

Hi there, I've run into an issue on my local galaxy install. When I have 20 or more datasets in my history, I no longer get the option to 'Enable/Disable selection of multiple input files...' I instead get a broken drop down list. I say broken because its as though the drop down list and input box have merged together. Is there a setting I need to change to correct this? Thanks Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Submitting jobs with PBS
by Marc Bras 29 May '12

29 May '12

Hi !! I've got a problem with PBS when I want to submit a job to our cluster with Galaxy. Every time, PBS says me "pbs_submit failed, PBS error 15023: Bad user - no password entry". Indeed, Galaxy uses my email address (used in Galaxy) as user by default ! But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner user and not my email… Is it possible to set the owner user as previous Galaxy version ? (I found the "drmaa_external_*" session in universe but I don't really understand how to configure this part…). Thanks a lot, Best Regards BRAS Marc

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BWA Problem
by CHEBBI Mohamed Amine 28 May '12

28 May '12

Hi ! I have a problem when i execute BWA from my local galaxy instance. I have this error message : An error occurred running this job:*BWA Version: 0.6.1-r104 Error indexing reference sequence. [bwa_index] Pack FASTA... 2.35 sec [bwa_index] Construct BWT for the packed sequence... Segmentation fault* * * Could anyone help me to fix it thanks ! Regards Amine

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Data file and Analysis Program versioning
by Wanmei 28 May '12

28 May '12

Hi All, I am pretty new to Galaxy. I would like to understand Galaxy's versioning capability from an end-user perspective (i do not mean the versioning capability that Mercurial offers in Galaxy repo). I did some research and found the following link mentioned a use case: if an end-user would like to rerun an analysis which was previously run using a different version of the analysis program, then Galaxy will prompt the end-user whether he/she would like to proceed with the new analysis. From this screenshot (in the link), it looks like Galaxy keeps track of the metadata of a output data file such as which analysis program and which version of the code produce it. is my understanding correct? http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions If the answer to my above question is yes, then i have one more question. does Galaxy version the output data as well? What i means is, for example, if the end-user agrees to use a newer version of the code to rerun (answer Yes to Galaxy's prompt), will the newly generated output be marked as version #2 as oppose to the original output (version #1)? Or it will just simply overwrites the previous analysis output file? Thanks, Wanmei

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how is metadata generated
by KOH Jia Yu Jayce 27 May '12

27 May '12

Hi Just wondering how metadata files in galaxy-dist/database/files/_metadata_files are generated? Are there any configurations in the xmls that specify these to be generated? Thanks

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