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.

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)
in samtools_sort.xml############################################
<command interpreter="sh">
discard_stderr_wrapper.sh samtools sort '$input' '$output'
</command>
##################################################################

Then I can success to finish the samtools sort job.
But I can not get sorted file from Galaxy interface.
Sorted file exists in the results folder as "dataset_97.dat.bam".
But it could not link on Galaxy.
Do you have any suggestion for this problem?

thanks
Masaki MS.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to