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 <jmchil...@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/af5577a24c155fa04aa607ff2fec283634df2fb0/raw
> -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.a...@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 <jmchil...@gmail.com> wrote:
>> 
>>> This looks very to similar to an issue discussed here:
>>> http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html.
>>> 
>>> The default branch of Galaxy contains changeset that should address
>>> this issue - 
>>> https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0.
>>> 
>>> Hope this helps.
>>> 
>>> -John
>>> 
>>> On Wed, Apr 2, 2014 at 11:35 AM, Ravi Alla <ravi.a...@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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>> 


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