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.
On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS <msmorioka-tky@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That wiki is out of date now, and should point you to the 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
On Wed, Nov 14, 2012 at 11:07 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS <msmorioka-tky@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That wiki is out of date now, and should point you to the 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
participants (2)
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Masaki MS -
Peter Cock