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.