If you are running jobs as "the real user" with drmaa (using the chown script) - you will probably want to setup a separate job destination using the local runner for upload jobs. The upload tool uses files that are created outside of Galaxy and these aren't modeled well.
Does this help?
On Fri, Mar 11, 2016 at 6:45 PM, Lemley, Rob email@example.com wrote:
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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