Wold Lab|
Size: 1188
Comment: added comments to bowtie template
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Size: 1709
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
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| 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 |
universe=vanilla |
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| Log = bowtie-submit.log.$(Process) Output = bowtie-submit.out.$(Process) Error = bowtie-submit.err.$(Process) |
environment="BOWTIE_INDEXES=/proj/genome/programs/bowtie-0.12.1/indexes OUTDIR=/full/path/to/output" executable=/proj/genome/programs/bowtie-0.12.1/bowtie arguments=hg19sp75spike -v 2 -k 11 -m 10 --best --strata -p 4 -q $OUTDIR/1184_1_1.fastq --un $OUTDIR/1184_1_1.unmapped.fa --max $OUTDIR/1185_1_1.repeat.fa $OUTDIR/1184_1_1.bowtie.txt log=bowtie.$(Process).log output=bowtie.$(Process).out error=bowtie.$(Process).err |
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| Queue | queue |
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| 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 |
universe=vanilla |
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| Log = makerdsfrombowtie-submit.log.$(Process) Output = makerdsfrombowtie-submit.out.$(Process) Error = makerdsfrombowtie-submit.err.$(Process) |
environment="ERANGEDIR=/path/to/erange/commoncode INDIR=/full/path/to/input OUTDIR=/full/path/to/output" |
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| Queue | executable = /usr/bin/python arguments = $ERANGEDIR/makerdsfrombowtie.py 1184_1_1 $INDIR/1184_1_1.bowtie.txt $OUTDIR/1184_1_1.rds -RNA $INDIR/hg19-knownGene.txt log=makerdsfrombowtie.$(Process).log output=makerdsfrombowtie.$(Process).out error=makerdsfrombowtie.$(Process).err queue |
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== Tophat Template == {{{ universe=vanilla environment="PATH=$PATH:/proj/genome/programs/bowtie-0.10.1:/proj/genome/programs/tophat-1.0.14/bin BOWTIE_INDEXES=/proj/genome/programs/bowtie-0.10.1/indexes INDIR=/full/path/to/input OUTDIR=/full/path/to/output" executable=/proj/genome/programs/bowtie-0.12.1/bowtie arguments="-p 4 -o $OUTDIR hg19 $INDIR/11501_61MMHAAXX.fa" error=tophat.$(PROCESS).err output=tophat.$(PROCESS).out log=tophat.$(PROCESS).log request_cpus=4 queue }}} |
Bowtie Template
universe=vanilla environment="BOWTIE_INDEXES=/proj/genome/programs/bowtie-0.12.1/indexes OUTDIR=/full/path/to/output" executable=/proj/genome/programs/bowtie-0.12.1/bowtie arguments=hg19sp75spike -v 2 -k 11 -m 10 --best --strata -p 4 -q $OUTDIR/1184_1_1.fastq --un $OUTDIR/1184_1_1.unmapped.fa --max $OUTDIR/1185_1_1.repeat.fa $OUTDIR/1184_1_1.bowtie.txt log=bowtie.$(Process).log output=bowtie.$(Process).out error=bowtie.$(Process).err request_cpus = 4 request_memory = 8000 request_disk = 0 queue
It's important to set the "request_cpus" variable to match the -p option to bowtie. It's also probably a good idea to set the "request_memory" to a more realistic value...8000 is almost 8 Gigs
ERANGE Template
universe=vanilla environment="ERANGEDIR=/path/to/erange/commoncode INDIR=/full/path/to/input OUTDIR=/full/path/to/output" executable = /usr/bin/python arguments = $ERANGEDIR/makerdsfrombowtie.py 1184_1_1 $INDIR/1184_1_1.bowtie.txt $OUTDIR/1184_1_1.rds -RNA $INDIR/hg19-knownGene.txt log=makerdsfrombowtie.$(Process).log output=makerdsfrombowtie.$(Process).out error=makerdsfrombowtie.$(Process).err queue
Tophat Template
universe=vanilla environment="PATH=$PATH:/proj/genome/programs/bowtie-0.10.1:/proj/genome/programs/tophat-1.0.14/bin BOWTIE_INDEXES=/proj/genome/programs/bowtie-0.10.1/indexes INDIR=/full/path/to/input OUTDIR=/full/path/to/output" executable=/proj/genome/programs/bowtie-0.12.1/bowtie arguments="-p 4 -o $OUTDIR hg19 $INDIR/11501_61MMHAAXX.fa" error=tophat.$(PROCESS).err output=tophat.$(PROCESS).out log=tophat.$(PROCESS).log request_cpus=4 queue