John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previous galaxy settings? Do I have to back up before I do this? I spent considerable time to get galaxy to work on the cluster and don't want to ruin it. Thank you Ravi On Apr 2, 2014, at 9:58 AM, John Chilton jmchilton@gmail.com wrote:

This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-un....

The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff....

Hope this helps.

-John

On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.alla@berkeley.edu wrote:

...

Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find.

galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 366, in monitor self.check_watched_items() File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *'

Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks

---

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Hi John, Thank you so much for this detailed explanation. Before I saw your email I went ahead and manually made changes in the pbs.py script. I didn't follow your mercurial commands and hope that is not a problem down the road (I guess I could use the hg revert option then).This seemed to have solved the problems I was seeing before. Cheers Ravi On Apr 2, 2014, at 7:47 PM, John Chilton jmchilton@gmail.com wrote:

This change is very small and was not committed to the stable branch of galaxy-central so I would just modify the your Galaxy's copy of the pbs runner file directly until the next release:

% wget https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff... -O /tmp/pbs.patch % hg import --no-commit /tmp/pbs.patch

When you go to update Galaxy next it will probably warn you that this file has been modified - at that time you can just run the following command to cleanup your Galaxy instance:

% hg revert lib/galaxy/jobs/runners/pbs.py

Hope this helps. The Galaxy team is actively discussing alternative ways to distribute fixes between large releases - hopefully I can stop e-mailing out random mercurial commands at some point :).

Back to your broader question however, the Galaxy release and update process is such that you really shouldn't lose your configuration as a result of updating Galaxy. Galaxy distributes sample tool_conf.xml, universe_wsgi.ini, etc... files but the actual configuration files themselves are not tracked in the Galaxy central repositories so these files should be unaffected by updates. Deviations from this ideal should be rare and I believe will be spelled out the dev news for releases as they occur. Hope this helps.

-John

On Wed, Apr 2, 2014 at 12:27 PM, Ravi Alla ravi.alla@berkeley.edu wrote:

...

John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previous galaxy settings? Do I have to back up before I do this? I spent considerable time to get galaxy to work on the cluster and don't want to ruin it. Thank you Ravi On Apr 2, 2014, at 9:58 AM, John Chilton jmchilton@gmail.com wrote:

...

This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-un....

The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff....

Hope this helps.

-John

On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla ravi.alla@berkeley.edu wrote:

...

Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find.

galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 366, in monitor self.check_watched_items() File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 363, in check_watched_items ( failures, statuses ) = self.check_all_jobs() File "/srv/www/galaxy/source/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 452, in check_all_jobs c = pbs.pbs_connect( pbs_server_name ) TypeError: in method 'pbs_connect', argument 1 of type 'char *'

Because of this error I cannot get any other jobs to run either. They just sit queued on the cluster. Any ideas? Thanks

---

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