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That wiki is out of date now, and should point you to the 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.

Peter
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