⇤ ← Revision 1 as of 2010-05-21 18:29:29
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Comment: added basic template for running bowtie with multiple threads
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991
Added template for ERANGE
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Deletions are marked like this. | Additions are marked like this. |
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== ERANGE Template == {{{ Executable = /usr/bin/python Arguments = /path/to/erange/commoncode/makerdsfrombowtie.py 1184_1_1 /path/to/bowtie_file/1184_1_1.bowtie.txt /path/to/rds_file/1184_1_1.rds -RNA /path/to/knownGene_file/hg19-knownGene.txt Log = makerdsfrombowtie-submit.log.$(Process) Output = makerdsfrombowtie-submit.out.$(Process) Error = makerdsfrombowtie-submit.err.$(Process) Queue }}} |
Bowtie Template
Executable = /proj/genome/programs/bowtie-0.12.1/bowtie Arguments = /proj/genome/programs/bowtie-0.12.1/indexes/hg19sp75spike -v 2 -k 11 -m 10 --best --strata -p 4 -q /full/path/to/fastq_file/1184_1_1.fastq --un /full/path/to/unmapped_file/1184_1_1.unmapped.fa --max /full/path/to/repeats_file/1185_1_1.repeat.fa /full/path/to/output_file/1184_1_1.bowtie.txt Log = bowtie-submit.log.$(Process) Output = bowtie-submit.out.$(Process) Error = bowtie-submit.err.$(Process) request_cpus = 4 request_memory = 8000 request_disk = 0 Queue
ERANGE Template
Executable = /usr/bin/python Arguments = /path/to/erange/commoncode/makerdsfrombowtie.py 1184_1_1 /path/to/bowtie_file/1184_1_1.bowtie.txt /path/to/rds_file/1184_1_1.rds -RNA /path/to/knownGene_file/hg19-knownGene.txt Log = makerdsfrombowtie-submit.log.$(Process) Output = makerdsfrombowtie-submit.out.$(Process) Error = makerdsfrombowtie-submit.err.$(Process) Queue