Commit 5ea97ae7 authored by Wai Yi Leung's avatar Wai Yi Leung

Merge branch 'fix-mac_unittests' into 'develop'

Added executables that are missing on a native osx install

Was installing ide on new mac book and did see some issues in the unit tests

See merge request !171
parents 24d9af80 dca682a1
...@@ -122,7 +122,10 @@ object ShivaTest { ...@@ -122,7 +122,10 @@ object ShivaTest {
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"macs2" -> Map("exe" -> "test"), "macs2" -> Map("exe" -> "test"),
"igvtools" -> 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( val sample1 = Map(
......
...@@ -125,6 +125,9 @@ object ShivaVariantcallingTest { ...@@ -125,6 +125,9 @@ object ShivaVariantcallingTest {
"gatk_jar" -> "test", "gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"bcftools" -> Map("exe" -> "test"), "bcftools" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test"),
"bgzip" -> Map("exe" -> "test"),
"tabix" -> Map("exe" -> "test"),
"input_alleles" -> "test" "input_alleles" -> "test"
) )
} }
\ No newline at end of file
...@@ -96,6 +96,7 @@ object BamMetricsTest { ...@@ -96,6 +96,7 @@ object BamMetricsTest {
"refFlat" -> "bla.refFlat", "refFlat" -> "bla.refFlat",
"reference_fasta" -> (outputDir + File.separator + "ref.fa"), "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"bedtools" -> Map("exe" -> "test") "bedtools" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test")
) )
} }
...@@ -119,7 +119,8 @@ object CarpTest { ...@@ -119,7 +119,8 @@ object CarpTest {
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"macs2" -> Map("exe" -> "test"), "macs2" -> Map("exe" -> "test"),
"igvtools" -> Map("exe" -> "test"), "igvtools" -> Map("exe" -> "test"),
"wigtobigwig" -> Map("exe" -> "test") "wigtobigwig" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test")
) )
val sample1 = Map( val sample1 = Map(
......
...@@ -101,6 +101,7 @@ object FlexiprepTest { ...@@ -101,6 +101,7 @@ object FlexiprepTest {
"fastqc" -> Map("exe" -> "test"), "fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"), "seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"), "sickle" -> Map("exe" -> "test"),
"cutadapt" -> Map("exe" -> "test") "cutadapt" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test")
) )
} }
...@@ -210,7 +210,7 @@ object GentrapTest { ...@@ -210,7 +210,7 @@ object GentrapTest {
// mapping executables // mapping executables
"star", "bowtie", "samtools", "gsnap", "tophat", "star", "bowtie", "samtools", "gsnap", "tophat",
// gentrap executables // gentrap executables
"cufflinks", "htseqcount", "grep", "pdflatex", "rscript", "tabix", "bgzip", "bedtoolscoverage", "cufflinks", "htseqcount", "grep", "pdflatex", "rscript", "tabix", "bgzip", "bedtoolscoverage", "md5sum",
// bam2wig executables // bam2wig executables
"igvtools", "wigtobigwig" "igvtools", "wigtobigwig"
).map { case exe => exe -> Map("exe" -> "test") }.toMap ).map { case exe => exe -> Map("exe" -> "test") }.toMap
......
...@@ -155,6 +155,7 @@ object MappingTest { ...@@ -155,6 +155,7 @@ object MappingTest {
"star" -> Map("exe" -> "test"), "star" -> Map("exe" -> "test"),
"bowtie" -> Map("exe" -> "test"), "bowtie" -> Map("exe" -> "test"),
"stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "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
...@@ -117,7 +117,10 @@ object ShivaTest { ...@@ -117,7 +117,10 @@ object ShivaTest {
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"macs2" -> Map("exe" -> "test"), "macs2" -> Map("exe" -> "test"),
"igvtools" -> 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( val sample1 = Map(
......
...@@ -106,6 +106,9 @@ object ShivaVariantcallingTest { ...@@ -106,6 +106,9 @@ object ShivaVariantcallingTest {
"gatk_jar" -> "test", "gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"), "samtools" -> Map("exe" -> "test"),
"bcftools" -> 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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