Hi John,
Thanks for getting back to me.
If I'm understanding the XML files correctly, the upload tool is already
configured to run as a local job. From job_conf.xml:
<tool id="upload1" destination="local" />
where "local" is our local job runner and "upload1" is defined in
data_source/upload.xml.
-Rob
Rob Lemley
Systems Administrator – CIRC
University of Rochester
-----Original Message-----
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: Tuesday, March 15, 2016 10:21 AM
To: Lemley, Rob <rob.lem...@rochester.edu>
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Problems uploading files to galaxy
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.lem...@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-boun...@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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