Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-25 Thread Raymond Wan
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

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Christian Brenninkmeijer
...@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 instal

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Briggs
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

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Cock
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

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
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. >

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
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

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Briggs
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

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Cock
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

[galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
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: