On Wed, Nov 14, 2012 at 11:07 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS <msmorioka-...@umin.ac.jp> wrote:
>> Dear all,
>>
>> I'm trying to set up samtools sort command on local Galaxy server.
>> But I can not success to get sorted files  from its result.
>
> I thought Galaxy tried to keep SAM/BAM files sorted by default...
>
>> First time, I got error message from Galaxy as..
>> error at..
>> [bam_sort_core] merging from 13 files...
>> To resolve this problem, I use discard_stderr_wrapper.sh for modifying my
>> samtools_sort.xml.
>> (http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr)
>
> That wiki is out of date now, and should point you to the <stdio>,
> <regex>, and <exit_code> tag sets documented here:
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax
>
> Using these new features you can avoid a wrapper script just to
> hide stderr.

Sorry - the wiki did link to the relevant page in the paragraph at the top.
Either I missed it or was seeing an older cache? In anycase, I've
reworded this page to try and make it clearer:
http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr

Peter
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