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

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

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