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bioinfo
ngs_tools
Commits
c068561a
Commit
c068561a
authored
Mar 13, 2017
by
Holger Brandl
Browse files
updated kotlin support API dependency
parent
f7692962
Changes
1
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Inline
Side-by-side
dge_workflow/star_align.kts
View file @
c068561a
#
!/
usr
/
bin
/
env
kscript
//DEPS de.mpicbg.scicomp
:joblist:0.7
de.mpicbg.scicomp:kutils:0.7
//DEPS de.mpicbg.scicomp
.joblist:joblist-kotlin:1.1
de.mpicbg.scicomp:kutils:0.7
// add docopts to local m2 index
...
...
@@ -7,7 +7,8 @@
// kotlinc-jvm -classpath $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT)
import
de.mpicbg.scicomp.kutils.evalBash
import
joblist.JobConfiguration
import
de.mpicbg.scicomp.kutils.joblist.JobConfig
import
de.mpicbg.scicomp.kutils.joblist.createHtmlReport
import
joblist.JobList
import
org.docopt.Docopt
import
java.io.File
...
...
@@ -131,11 +132,9 @@ for (fastqFile in fastqFiles) {
samtools index ${fastqBaseName}.bam
"""
.
trimIndent
()
// todo provide proper walltime here
// slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
// sacct -o MaxRSS -j JOBID
jl
.
run
(
JobConfiguration
(
cmd
,
"star__${fastqBaseName}"
,
"10:00"
,
""
,
5
,
40000
,
""
,
better
.
files
.
File
(
File
(
"."
).
toPath
())))
// jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, 0, "", better.files.File(File(".").toPath())))
jl
.
run
(
JobConfig
(
cmd
,
"star__${fastqBaseName}"
,
"10:00"
,
""
,
5
,
40000
))
}
...
...
@@ -145,7 +144,7 @@ jl.waitUntilDone(1000)
// http://lampwww.epfl.ch/~michelou/scala/using-scala-from-java.html
j
oblist
.
`package
$`
.
`MODULE
$`
.
ImplJobListUtils
(
jl
)
.
createHtmlReport
()
j
l
.
createHtmlReport
()
//// estimate expresssion with http://bioinf.wehi.edu.au/featureCounts/
...
...
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