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

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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