To follow up on what Peter says

It is the code in 
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py
from line 182
class Bam( Binary ):

This code (set_meta) is called after the tool has finished running while it is 
copying the resulting data into the galaxy database.
If the bam file is unsorted or incorrectly sorted any tool fails.

But if the _get_samtools_version methods found the early version of samtools it 
crashed our galaxy.

2 issues here.
1. Galaxy will only handle sorted bam files (regrettable but that is political)
2. While galaxy has wheels (previously eggs) for all other dependencies it 
relies on locally installed samtools.  Can this really not be fixed???????

Christian
University of Manchester


________________________________________
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Peter Briggs [peter.bri...@manchester.ac.uk]
Sent: Tuesday, May 24, 2016 12:04 PM
To: Raymond Wan
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

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

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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