I believe the following changeset fixes this problem. https://bitbucket.org/jmchilton/galaxy-central-lwr/commits/3b6c209d2d078bad2... I have incorporated the fix into pull request 138 that has other job runner fixes and enhancements. -John P.S. Peter's point about the tasked job runner being frequently broken is a good one, it has been broken more often than not over the last 6 months. Digging through Trello it is clear the same applies to composite datatypes. If only there was a big important feature that depended on these that we could push through to ensure these enhancements that are important to the community got more attention :). On Sun, Mar 17, 2013 at 11:00 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sun, Mar 17, 2013 at 3:40 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Am Sonntag, den 17.03.2013, 15:26 +0000 schrieb Peter Cock:
On Sun, Mar 17, 2013 at 3:13 PM, Björn Grüning wrote:
Hi all,
can anyone confirm that the parallelism features is not working in galaxy-central? Parallelism is among others used by the blast+ wrappers.
The only error message I get is:
galaxy.jobs DEBUG 2013-03-17 16:08:27,729 (64174) Working directory for job is: /media/data/web/galaxy-central/database/job_working_directory/064/64174 galaxy.jobs.handler DEBUG 2013-03-17 16:08:27,750 (64174) Dispatching to tasks runner galaxy.jobs.handler ERROR 2013-03-17 16:08:27,750 put(): (64174) Invalid job runner: tasks galaxy.datatypes.metadata DEBUG 2013-03-17 16:08:28,079 Cleaning up external metadata files galaxy.jobs.handler INFO 2013-03-17 16:08:28,120 (64174) Job dispatched
It's working fine for me with galaxy-dist. Thanks! Bjoern
Which hg revision are you on from galaxy-central? It was working for me last time I tested, but my setup isn't fully up-to-date with the development repository.
I'm on 9088:1aa6224b32c2. Which hg revision are you using? Maybe I can track down the commit. handler.py changed a lot recently :(
So yours is very up to date, just 20 hours ago according to bitbucket: https://bitbucket.org/galaxy/galaxy-central/commits/1aa6224b32c2
For the default branch (which I merge into my working branch), I last updated 24 days ago - over three weeks: https://bitbucket.org/galaxy/galaxy-central/commits/45f1d93124ad
$ hg id 45f1d93124ad
$ hg log -l 1 -b default changeset: 9548:45f1d93124ad parent: 9546:1adf6fdd9c49 user: InitHello <inithello@gmail.com> date: Thu Feb 21 11:06:11 2013 -0500 summary: Changed to_safe_string to use markupsafe.escape for unsafe characters.
Assuming I'm right and parallelism was working fine with that commit, we've only narrowed this down to the last 24 days. If I update mine and it breaks, I'll let you know.
Peter
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