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 recover
...@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 installe
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 inst
On Tue, May 24, 2016 at 11:42 AM, Raymond Wan wrote:
> Hi Peter,
>
>
> On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote:
>> In case you didn't know, Galaxy likes to keep all BAM files in
>> coordinate sorted order with a BAI index (using samtools).
>> Somehow this is failing on your system (perh
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Briggs
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 samto
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote:
> In case you didn't know, Galaxy likes to keep all BAM files in
> coordinate sorted order with a BAI index (using samtools).
> Somehow this is failing on your system (perhaps a suitable
> version of samtools is not on the $PATH).
No
Hello Ray
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
Hi Raymond,
In case you didn't know, Galaxy likes to keep all BAM files in
coordinate sorted order with a BAI index (using samtools).
Somehow this is failing on your system (perhaps a suitable
version of samtools is not on the $PATH).
I'm sure a Galaxy expert can and will comment, but it looks li
Dear all,
We are experiencing a crash of our Galaxy instance (latest git log is
early January 2016) and it seems unable to restart. The last entries
in paster.log says the following:
galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling
'histories' API controller, class: HistoriesCon
