Commit dca682a1 authored by Peter van 't Hof's avatar Peter van 't Hof

Added executables that are missing on a native osx install

parent 67e03c46
......@@ -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(
......
......@@ -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
......@@ -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")
)
}
......@@ -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(
......
......@@ -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")
)
}
......@@ -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
......
......@@ -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
......@@ -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(
......
......@@ -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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