Thanks Peter, that's really helpful. I'm glad we're not the only ones running into this. -Rob Rob Lemley Systems Administrator – CIRC University of Rochester -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: Tuesday, March 15, 2016 10:34 AM To: John Chilton <jmchilton@gmail.com> Cc: Lemley, Rob <rob.lemley@rochester.edu>; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Problems uploading files to galaxy On Tue, Mar 15, 2016 at 2:21 PM, John Chilton <jmchilton@gmail.com> wrote:
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
We found the opposite - if using "the real user", the Galaxy v16.01 would do a chown on the datafiles for DRMAA jobs (good) but also for local jobs (bad): https://urldefense.proofpoint.com/v2/url?u=http-3A__dev.list.galaxyproject.org_external-2Dchown-2Dscript-2Dpy-2Dand-2Dthe-2Dlocal-2Djob-2Drunner-2Dtt4668738.html&d=BQIBaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=d-Zn2Sbc-XheRlOYkSFXPupZ8ZmuYq52isQBiI3MBWA&m=rMI9zRSmgepuzJAMtXaa8aFFhpcuYbKx2r_h3aC6wIg&s=IZ8BQgQLJhvOnBc_xzGzMYMVVETGgFUhcBM_tNlMXRE&e= I will reply on that thread now with an update... Peter