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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