Hi, Nicola is right But I believe that your outputs aren't correctly declared. files_path keep all your files in their original directory. It's usefull when you want to build a HTML page to wrap your several outputs. In your case, I propose this command line <command detect_errors="aggressive"><![CDATA[ python /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o . -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 && mv alignments.bam $alignments && mv deletions.txt $deletions && mv insertions.txt $insertions && mv ....... ]]</command> Must be completed and tested Cheers Gildas Le 29/10/2015 17:21, Nicola Soranzo a écrit :

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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