On Mon, Jul 8, 2013 at 3:36 PM, Nicholas Kline <nx...@case.edu> wrote:
> Hi,
> Our lab recently installed a local version of Galaxy on a mid-2012 Mac
> Pro computer. We can access the Galaxy server and sign in as an
> administrator. Today we tried creating a Data Library, adding a
> dataset to it, and uploading a directory of files. We followed this
> Galaxy documentation (
> http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?action=show&redirect=Admin%2FData+Libraries%2FUploading+Library+Files
> ) to setup this feature:
> - Admin > Data Library > Add datasets > Upload directory of files
> - file format was set to auto-detect
> - and we chose the option to link to files instead of copying them
> Galaxy confirmed that the files were successfully uploaded. However,
> in the data library, under the Message column, is a message in red
> saying "Job error (click name for more info)". Clicking on one of the
> uploaded files displays a page with this information:
> Date uploaded: 2013-06-28
> File size: 7.5 GB
> Data type: auto
> Build: sacCer2
> Miscellaneous information:
> Traceback (most recent call last): File
> "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line
> 386, in __main__() File
> "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line
> 357, in __main__ output_paths =
> Job Standard Error
> Traceback (most recent call last):
> File "/Users/administrator/galaxy-dist/tools/data_source/upload.py",
> line 386, in
> __main__()
> File "/Users/administrator/galaxy-dist/tools/data_source/upload.py",
> line 357, in __main__
> output_paths = parse_outputs( sys.argv[4:] )
> File "/Users/administrator/galaxy-dist/tools/data_source/upload.py",
> line 64, in parse_outputs
> id, files_path, path = arg.split( ':', 2 )
> ValueError: need more than 1 value to unpack
> error
> Database/Build: sacCer2
> Number of data lines: None
> Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq

I have a hunch that the problem could be related to the spaces
in the input filename. In this case perhaps the upload.py script
is being called without the filename being quoted or escaped.
Could you retry from a nice space free import directory?

Also does the path where you have installed Galaxy have
spaces? Even if Galaxy itself copes, it is highly likely that
one or more underlying tools wrapped for use within Galaxy
would fail.

[I've had minor problems with this with various tools on the
Mac outside of Galaxy usage]


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