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 !
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/