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 job submission 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.