Activity for John Martin
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John Martin posted a comment on discussion PBJelly Tickets
Just wanted to report back that LSF works fine for PBSuite, my problem was just some bad syntax
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And actually, if it doesn't support LSF could I manually run all the shell scripts in such a way that PBJelly could pick up and continue on with the steps after mapping?
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I'm trying to submit the mapping portion of pbjelly to an LSF cluster (using 'bsub'). I've split the subreads fastq into 200 parts and I had thought I setup the Protocols.xml file correctly. But when I run Jelly.py mapping Protocol.xml it builds all the shell scripts but doesn't launch anything. Does PBJelly support LSF/bsub? Here is how I setup my cluster command: <cluster> echo '${CMD}' | bsub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -n 200 -M 31000000 -R 'rusage[mem=30000]' -a 'docker(jmartin7/ubuntu:pbsuite)'...
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