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.
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