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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