I didn’t see any response to my email below. Does anyone have any thoughts? I'm pretty stuck.
Rob Lemley Systems Administrator – CIRC University of Rochester
-----Original Message----- From: galaxy-dev [mailto:firstname.lastname@example.org] On Behalf Of Lemley, Rob Sent: Monday, March 7, 2016 2:03 PM To: email@example.com Subject: [galaxy-dev] Problems uploading files to galaxy
I'm hoping you can help out with a problem we are experiencing uploading files to our own Galaxy instance.
When a user tries to upload a file to Galaxy through their web browser, the job errors out:
Traceback (most recent call last): File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 430, in <module> __main__() File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 407, in __main__ for line in open( sys.argv, 'r' ): IOError: [Errno 13] Permission denied: '/scratch/XXXXXX/XXXXXX/galaxy/tmp/tmpSlG2pC'
The permissions on the referenced file: -rw-------+ 1 rlemley rlemley 317 Mar 7 13:42 tmpSlG2pC
As the Galaxy daemons run as XXXXXX_galaxy, it does not have permission to read the file.
I tried modifying external_chown_script.py so that XXXXXX_galaxy has permission to read that file, but that caused problems elsewhere so I backed out the changes.
Rob Lemley Systems Administrator - CIRC University of Rochester
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