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 That wiki is out of date now, and should point you to the 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