Hello Ray

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


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!


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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