Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
2d3a083a
Commit
2d3a083a
authored
Aug 23, 2016
by
Peter van 't Hof
Browse files
Added igvtools_jar to mock config
parent
0da332ac
Changes
5
Hide whitespace changes
Inline
Side-by-side
carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
2d3a083a
...
...
@@ -125,7 +125,7 @@ object CarpTest {
"bwa"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
)
)
...
...
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
2d3a083a
...
...
@@ -194,6 +194,7 @@ object GentrapTest {
"ribosome_refflat"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"varscan_jar"
->
"test"
,
"rscript"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"gatk_jar"
->
"test"
)
++
Seq
(
// fastqc executables
...
...
@@ -203,7 +204,7 @@ object GentrapTest {
// gentrap executables
"cufflinks"
,
"htseqcount"
,
"grep"
,
"pdflatex"
,
"rscript"
,
"tabix"
,
"bgzip"
,
"bedtoolscoverage"
,
"md5sum"
,
// bam2wig executables
"igvtools"
,
"wigtobigwig"
"wigtobigwig"
).
map
{
case
exe
=>
exe
->
Map
(
"exe"
->
"test"
)
}.
toMap
val
sample1
:
Map
[
String
,
Any
]
=
Map
(
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
2d3a083a
...
...
@@ -194,7 +194,7 @@ object MultisampleMappingTestTrait {
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
2d3a083a
...
...
@@ -210,7 +210,7 @@ object ShivaTest {
"bwa"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"macs2"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
...
...
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
View file @
2d3a083a
...
...
@@ -134,7 +134,7 @@ object TinyCapTest {
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"htseqcount"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
)
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment