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