Hello Peter and everyone,

Just wanted to update all of you that replacing samtools with 1.2
solved the problem.  As you suggested, we didn't replace the
system-installed one at /usr/bin (though I suppose we could have) but
modified the environment variable.

I don't know the details of the recovery since I look after Galaxy and
not the overall system (i.e., I'm not the root user) but it sounds
like the administrators didn't need to perform any job deletions
and/or Galaxy database editing.  Once samtools was replaced, the
system managed to restart correctly.

Honestly, we never would have guessed that using an old version of
samtools would cause Galaxy to crash.  Even with the log files
alluding to it, we were initially in disbelief.

And thanks to Christian for pointing out the main cause of the problem
in the source code.  We had thought (hoped?) that Galaxy was a
self-contained system.  So, this experience helped us better
understand how Galaxy works.

Thank you all for your prompt help!


On Tue, May 24, 2016 at 7:04 PM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> Just to clarify, for us it wasn't dependent on the tool - it was actually
> the version of samtools installed in the 'galaxy' user's environment i.e. on
> the 'galaxy' user's PATH.
> I set it explicitly by creating a file called "local_env.sh" in the 'config'
> directory of the Galaxy installation with the following content:
> $ cat local_env.sh
> # Prepend samtools 1.2
> export PATH=$HOME/apps/samtools/1.2/bin:$PATH
> ##
> #
> which is automatically picked up by 'run.sh' when Galaxy is started (I don't
> know how that plays if you're using a uwsgi/supervisor setup).
> Best wishes
> Peter
> On 24/05/16 11:46, Raymond Wan wrote:
>> Hi Peter,
>> On Tue, May 24, 2016 at 6:29 PM, Peter Briggs
>> <peter.bri...@manchester.ac.uk> wrote:
>>> One of my colleagues encountered a similar-sounding error on our local
>>> test
>>> instance, where an unsorted BAM file seemed to crash the Galaxy handler
>>> processes and prevented them from restarting.
>>> In our case the default samtools version in the Galaxy environment was
>>> 0.1.18; we found that updating this to samtools 1.2 fixed the crash
>>> problem.
>> Ah!  That does sound familiar.  As I just replied in another message,
>> we seem to have at least 5 versions of samtools in the system.  I'm
>> not sure if that is normal or not for a Galaxy instance...
>> Let me see if I can figure out (through logs, but most likely by
>> asking the user) what tool he was using and figure out which samtools
>> executable was being run.  If it is 0.1.18, I'll look into update
>> it...thank you for sharing your colleague's experience!
>> Ray
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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