Thanks Nate, I couldn't find a logfile in the galaxy-dist directory.Where is it located? However,  when I redid the library upload operation it did not produce any errors. I believe, it my mistake in uploading. The files were located on an nfs server, which is somewhat slow, and I have migrated to another page before the library upload was complete. I thought the process would get completed in background and navigated away to another page. This time, I waited till the process was complete. There were no errors. Thanks.   -- 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

...

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