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(a)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(a)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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.galaxyproject....
To search Galaxy mailing lists use the unified search at:
https://urldefense.proofpoint.com/v2/url?u=http-3A__galaxyproject.org_sea...
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/