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biopet.biopet
Commits
dca682a1
Commit
dca682a1
authored
Jun 21, 2015
by
Peter van 't Hof
Browse files
Added executables that are missing on a native osx install
parent
67e03c46
Changes
9
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
dca682a1
...
...
@@ -122,7 +122,10 @@ object ShivaTest {
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
)
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
)
)
val
sample1
=
Map
(
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
dca682a1
...
...
@@ -125,6 +125,9 @@ object ShivaVariantcallingTest {
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"input_alleles"
->
"test"
)
}
\ No newline at end of file
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
dca682a1
...
...
@@ -96,6 +96,7 @@ object BamMetricsTest {
"refFlat"
->
"bla.refFlat"
,
"reference_fasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"bedtools"
->
Map
(
"exe"
->
"test"
)
"bedtools"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
}
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
dca682a1
...
...
@@ -119,7 +119,8 @@ object CarpTest {
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
)
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
val
sample1
=
Map
(
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
dca682a1
...
...
@@ -101,6 +101,7 @@ object FlexiprepTest {
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
)
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
}
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
dca682a1
...
...
@@ -210,7 +210,7 @@ object GentrapTest {
// mapping executables
"star"
,
"bowtie"
,
"samtools"
,
"gsnap"
,
"tophat"
,
// gentrap executables
"cufflinks"
,
"htseqcount"
,
"grep"
,
"pdflatex"
,
"rscript"
,
"tabix"
,
"bgzip"
,
"bedtoolscoverage"
,
"cufflinks"
,
"htseqcount"
,
"grep"
,
"pdflatex"
,
"rscript"
,
"tabix"
,
"bgzip"
,
"bedtoolscoverage"
,
"md5sum"
,
// bam2wig executables
"igvtools"
,
"wigtobigwig"
).
map
{
case
exe
=>
exe
->
Map
(
"exe"
->
"test"
)
}.
toMap
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
dca682a1
...
...
@@ -155,6 +155,7 @@ object MappingTest {
"star"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
,
"genome"
->
"test"
,
"hash"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
)
"samtools"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
}
\ No newline at end of file
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
dca682a1
...
...
@@ -117,7 +117,10 @@ object ShivaTest {
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
)
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
)
)
val
sample1
=
Map
(
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
dca682a1
...
...
@@ -106,6 +106,9 @@ object ShivaVariantcallingTest {
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
"freebayes"
->
Map
(
"exe"
->
"test"
)
"freebayes"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
)
)
}
\ No newline at end of file
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