Re: [galaxy-dev] [galaxy-user] Data Library Import "tool error"

-- With Regards, Sridhar ----- Message from nate@bx.psu.edu ---------     Date: Tue, 30 Nov 2010 16:27:19 -0500     From: Nate Coraor nate@bx.psu.edu Reply-To: Nate Coraor nate@bx.psu.edu Subject: Re: [galaxy-user] Data Library Import "tool error"       To: Sridhar A Malkaram smalkaram2@unl.edu       Cc: Galaxy Dev galaxy-dev@bx.psu.edu > Sridhar A Malkaram wrote: >> >> >>    Hi, >> >>    I used the "Upload files from filesystem paths" option to upload a >> directory path into Galaxy Data library. I used the option NO for >> "Copy data into Galaxy?" as I don't want a duplicate copy of the >> data. I selected the hg19 for Genome. After the upload process is >> finished, I can see the directory tree structure, but in the >> "information" column for files, it reports "Job error (click name >> for more info)". >> >>    When I click a file, for example for "macs_test_1_out.bed",  which >> is a bed filetype, it says "failure running job  tool error" under >> "Miscellaneous information". I am pasting below the whlole >> information. >> >>    This happens for all the data files that are uploaded. What is >> this error? and which tool it is complaining about? > > Hi Sridhar, > > Since this question concerns a local installation of Galaxy, I've moved > it over to the galaxy-dev list. > > Is there anything displayed in Galaxy's server log when this failure > occurs? > >>    My another question is, can we upload files/directories with >> compressed format files (.tar, .gz, .bz. etc) and binary files like >> .doc, .xls ? If so, what additional plugins we need to have in >> place? > > Single-file zip and tar(.gz or .bz2) files can be uploaded, as well as > directly compressed .gz and .bz2 files.  All of these, however, will be > decompressed upon uploading. > > I believe someone made a datatype for .xls, but it is not part of the > Galaxy distribution. > > --nate > >> >>    Thanks in advance for your suggestions. >> >>     ================================ Message: >> >>    Galaxy Test-data   Uploaded by:    Date uploaded: 2010-11-29 >> File size: 52.2 Kb   Data type: data   Build: hg19   Miscellaneous >> information: failure running job   tool error   Database/Build: hg19 >> Peek: >> >>    Disk file:  >> /mnt/bioinfo/LINKS/Biotin/data/work/galaxy-dist/test-data/peakcalling_macs/macs_test_1_out.bed >> >>    ================================ >> >>    -- >> With Regards, >> >> Sridhar >> Postdoctoral Research Associate >> Nutrition and Health Sciences >> University of Nebraska-Lincoln >> >> > >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user@lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user%5B1] > ----- End message from nate@bx.psu.edu ----- Links: ------ [1] http://lists.bx.psu.edu/listinfo/galaxy-user