Wold Lab|
Size: 1188
Comment: added comments to bowtie template
|
Size: 2728
Comment: added blurb about file transfers
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| == A Quick Word on Files == Condor has the ability to work with files which live on the NFS server (castor, loxcyc, rattus) as well as files local to the execute host. If you plan to work with a ton of small files or a handful of large files, feel free to use the NFS server as the source for your files. If you have a bunch of large files to process, you'll likely be better off telling Condor to transfer the files to the execute host before executing your job. Not only will you get better performance, everyone else will still be able to use the NFS server, allowing you to save face at the same time...Trust me, I speak from experience. To transfer files to the execute host, use the following directives: {{{ should_transfer_files = YES when_to_transfer_output = ON_EXIT transfer_input_files = /full/path/to/infile1,/full/path/to/infile2,... }}} This can be done globally by placing these directives at the top of the recipe, or on a per-job basis by placing them before each "queue" directive. |
|
| Line 3: | Line 15: |
| 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 |
| Line 6: | Line 17: |
| 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 |
| Line 14: | Line 30: |
| Queue | queue |
| Line 21: | Line 37: |
| 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 |
| Line 24: | Line 39: |
| 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" |
| Line 28: | Line 41: |
| 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 |
| Line 30: | Line 50: |
== 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 }}} |
A Quick Word on Files
Condor has the ability to work with files which live on the NFS server (castor, loxcyc, rattus) as well as files local to the execute host. If you plan to work with a ton of small files or a handful of large files, feel free to use the NFS server as the source for your files. If you have a bunch of large files to process, you'll likely be better off telling Condor to transfer the files to the execute host before executing your job. Not only will you get better performance, everyone else will still be able to use the NFS server, allowing you to save face at the same time...Trust me, I speak from experience.
To transfer files to the execute host, use the following directives:
should_transfer_files = YES when_to_transfer_output = ON_EXIT transfer_input_files = /full/path/to/infile1,/full/path/to/infile2,...
This can be done globally by placing these directives at the top of the recipe, or on a per-job basis by placing them before each "queue" directive.
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