Hi Yoong,
I think your tool is writing its logging messages on stderr, which causes Galaxy to mark the job as failed.


I think that adding detect_errors="aggressive" to your <command> should fix it, see https://github.com/galaxyproject/galaxy/pull/117 for details.

Cheers,
Nicola

On 29/10/15 00:24, 홍윤지 wrote:
Hello, My name is yoong in korean Student

I try to use the program namd mapsplice2 on galaxy, but

when i write the xml file, i got a problom...
the xml file located same place with mapspclie.py

And mapsplice has not single output file, so i put the -o option like this

python /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o $alignments.files_path -p 10 --qual-scale phred33 --bam --fusion -c /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 $input_reads_1 -2 $input_reads_2


the mapsplice2 needs 2 input file, and 2 referens file , then make 8 output files include log folder.


if i use that command, result has came out, but it's alwasy failed ... T_T


Thank you so much ! Have a nice day !


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