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

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