Mercurial > repos > devteam > bowtie_wrappers
changeset 2:42c4463baaad draft
Convert tool to use $GALAXY_SLOTS if available.
| author | Nate Coraor <nate@bx.psu.edu> |
|---|---|
| date | Thu, 16 Jan 2014 13:08:38 -0500 |
| parents | e1c59c194b7b |
| children | 9ca609a2a421 |
| files | bowtie_wrapper.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/bowtie_wrapper.xml Mon Apr 01 14:36:33 2013 -0400 +++ b/bowtie_wrapper.xml Thu Jan 16 13:08:38 2014 -0500 @@ -6,8 +6,8 @@ <parallelism method="basic"></parallelism> <command interpreter="python"> bowtie_wrapper.py - ## Hackish setting of number of threads - --threads="4" + ## Set number of threads + --threads="\${GALAXY_SLOTS:-4}" ## Outputs --output="${output}" #if str( $singlePaired.sPaired ) == "single" @@ -449,7 +449,7 @@ Bowtie command: bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam sort bowtie_out6_u.sam > bowtie_out6.sam - -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. + -p is the number of threads. You need to replace the + with 2 dashes. chrM_base needs to be the base location/name of the index files. --> <param name="genomeSource" value="indexed" /> @@ -470,7 +470,7 @@ sort bowtie_out8_u_1.sam > bowtie_out8_1.sam sort bowtie_out8_u_2.sam > bowtie_out8_2.sam Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. - -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. + -p is the number of threads. You need to replace the + with 2 dashes. The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. chrM_base is the index files' location/base name. --> @@ -597,7 +597,7 @@ Bowtie command: bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam sort bowtie_out9_u.sam > bowtie_out9.sam - -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. + -p is the number of threads. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="indexed" /> @@ -634,7 +634,7 @@ bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam sort bowtie_out10_u.sam > bowtie_out10.sam - -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. + -p is the number of threads. You need to replace the + with 2 dashes. chrM_base is the index files' location/base name. --> <param name="genomeSource" value="history" />