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bioinfo
ngs_tools
Commits
dc74d040
Commit
dc74d040
authored
9 years ago
by
Holger Brandl
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added start tests
parent
6b5fcd52
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dge_workflow/star_align.kts
+18
-8
18 additions, 8 deletions
dge_workflow/star_align.kts
dge_workflow/testdata/featcounts_deseq/test_star.sh
+15
-0
15 additions, 0 deletions
dge_workflow/testdata/featcounts_deseq/test_star.sh
with
33 additions
and
8 deletions
dge_workflow/star_align.kts
+
18
−
8
View file @
dc74d040
...
...
@@ -42,12 +42,19 @@ val igenome = File(doArgs["igenome"])
val
star_index
=
File
(
igenome
,
"Sequence/StarIndex"
)
val
gtfFile
=
if
(
doArgs
[
"gtfFile"
]
!=
null
)
File
(
doArgs
[
"gtfFile"
])
else
File
(
igenome
,
"Annotation/Genes/genes.gtf"
)
println
(
"validating inputs..."
)
println
(
"validating system requirements..."
)
// make sure that STAR is in the PATH
if
(
evalBash
(
"which STAR"
).
exitCode
!=
0
)
throw
IllegalArgumentException
(
"STAR aligner is not in PATH"
)
System
.
getenv
(
"NGS_TOOLS"
).
let
{
require
(
it
.
isNotBlank
()
&&
File
(
it
).
isDirectory
)
{
"NGS_TOOLS is not defined but needed to locate star_qc.R"
}
}
require
(
evalBash
(
"type dge_star_counts2matrix"
).
exitCode
==
0
)
{
"dge_star_counts2matrix is missing"
}
require
(
evalBash
(
"type dge_bam_correlate"
).
exitCode
==
0
){
"dge_bam_correlate is missing"
}
println
(
"validating inputs..."
)
// check if gtf file exists
if
(!
gtfFile
.
isFile
())
throw
IllegalArgumentException
(
"gtf '${gtfFile}' does not exist"
)
...
...
@@ -112,11 +119,14 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
// cleanup
evalBash
(
"""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out"""
)
//
Test
for bam correlation (but don't wait for the results)
//
Do reporting and per
for
m
bam correlation (but don't wait for the results)
evalBash
(
"""
rend.R - e ${ System.getenv("NGS_TOOLS") } / dge_workflow / star_qc.R.
dge_bam_correlate &
"""
)
rend.R - e ${'$'}NGS_TOOLS / dge_workflow / star_qc.R.
// Condense counts into matrix
evalBash
(
"""dge_star_countas2matrix"""
)
# Condense counts into matrix
dge_star_counts2matrix
# http://superuser.com/questions/178587/how-do-i-detach-a-process-from-terminal-entirely
nohup dge_bam_correlate &
#dge_bam_correlate &
"""
)
This diff is collapsed.
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dge_workflow/testdata/featcounts_deseq/test_star.sh
0 → 100644
+
15
−
0
View file @
dc74d040
screen
-R
star_test
cd
/home/brandl/test_star_kot
export
NGS_TOOLS
=
"/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/dev"
export
PATH
=
/home/brandl/bin/STAR-2.5.1b/source:
$PATH
export
PATH
=
${
NGS_TOOLS
}
/dge_workflow:
$PATH
source
$NGS_TOOLS
/dge_workflow/dge_utils.sh
#git clone https://github.com/holgerbrandl/kutils && cd kutils && gradle install && cd .. && rm -rf kutils
star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 test.fastq
mailme
"test"
\ No newline at end of file
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