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? -John On Fri, Mar 11, 2016 at 6:45 PM, Lemley, Rob <rob.lemley@rochester.edu> wrote:
Hi everyone,
I didn’t see any response to my email below. Does anyone have any thoughts? I'm pretty stuck.
Thanks again,
-Rob
Rob Lemley Systems Administrator – CIRC University of Rochester
-----Original Message----- From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Lemley, Rob Sent: Monday, March 7, 2016 2:03 PM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Problems uploading files to galaxy
Hi,
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[3], '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.
Any suggestions?
Many thanks,
-Rob
Rob Lemley Systems Administrator - CIRC University of Rochester
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