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:
-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
-R /bio-db/reference-genome/hg19.fa -T DepthOfCoverage
But I got an error message like this: gatk_wrapper.py: error: no such
Then I tried to add a couple of single quotes on the parameters behind of
-d and -p, just like the following:
-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
-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!
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