Dear everyone,

These days I want to  localize Galaxy on our server. When I tried to
arrange gatk, I met a problem as follow. Firstly, I run the script
'gatk_wrapper.py' like this:

python
/bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/tools/gatk/gatk_wrapper.py
-d  -I /share/home/wuyilei/bioc/test/111/test1.bbioc/test/111/test1.bam
.bam test1 -p  /bio-db/apps/pool/java1.6/jre1.6.0_24/bin/java -jar
/bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/shared/jars/gatk/GenomeAnalysisTK.jar
-R /bio-db/reference-genome/hg19.fa -T  DepthOfCoverage

But I got an error message like this:       gatk_wrapper.py: error: no such
option: -j

Then I tried to add a couple of single quotes on the parameters  behind of
-d and -p, just like the following:

python
/bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/tools/gatk/gatk_wrapper.py
-d  '-I' /share/home/wuyilei/bioc/test/111/test1.bbioc/test/111/test1.bam
.bam test1 -p  '/bio-db/apps/pool/java1.6/jre1.6.0_24/bin/java -jar
/bio-db/apps/api/galaxy-galaxy-dist-e6444e7a1685/shared/jars/gatk/GenomeAnalysisTK.jar
-R /bio-db/reference-genome/hg19.fa -T  DepthOfCoverage '

Then 'gatk_wrapper.py' can work well!

But if I use the ob scheduling system which was arranged on my server, I
can not run the 'gatk_wrapper.py' script any more. After a long time
research, I found the problem, all because  of the  single quotes behind of
-d and -p.

Can anyone help me, for example, rewrite the script  'gatk_wrapper.py' for
me, then I can delete the single quotes! Or give me some other advice.

Looking forward your reply!

Best,
Wei Liu.
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