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bioinfo
ngs_tools
Commits
68beea46
Commit
68beea46
authored
8 years ago
by
Holger Brandl
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Merge remote-tracking branch 'remotes/origin/master' into madmax
parents
d3488019
398c04b4
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dge_workflow/star_align.kts
+7
-3
7 additions, 3 deletions
dge_workflow/star_align.kts
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7 additions
and
3 deletions
dge_workflow/star_align.kts
+
7
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3
View file @
68beea46
#
!/
usr
/
bin
/
env
kscript
//DEPS org.docopt:docopt:0.6.0-SNAPSHOT de.mpicbg.scicomp:joblist_2.11:0.6-SNAPSHOT de.mpicbg.scicomp.bioinfo:kutils:0.1-SNAPSHOT
//DEPS com.offbytwo:docopt:0.6.0.20150202 de.mpicbg.scicomp:joblist:0.6-SNAPSHOT de.mpicbg.scicomp.bioinfo:kutils:0.1-SNAPSHOT
// add docopts to local m2 index
// git clone https://github.com/docopt/docopt.java && cd docopt.java && mvn clean package install -Dmaven.test.skip=true
...
...
@@ -97,7 +98,10 @@ for (fastqFile in fastqFiles) {
samtools index ${fastqBaseName}.bam
"""
.
trimIndent
()
jl
.
run
(
JobConfiguration
(
cmd
,
"star__${fastqBaseName}"
,
""
,
"medium"
,
5
,
""
,
better
.
files
.
File
(
File
(
"."
).
toPath
())))
// todo provide proper walltime here
// slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
// sacct -o MaxRSS -j JOBID
jl
.
run
(
JobConfiguration
(
cmd
,
"star__${fastqBaseName}"
,
"5:00:00"
,
""
,
5
,
"--mem 40000"
,
better
.
files
.
File
(
File
(
"."
).
toPath
())))
}
...
...
@@ -122,7 +126,7 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
// cleanup
evalBash
(
"rm -
rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out"
)
evalBash
(
"rm -rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out"
)
// Do reporting and perform bam correlation (but don't wait for the results)
...
...
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