cnvnator is now cnvnator-multi, updated config

.gitignore

@@ -3,7 +3,7 @@
 bin/bedpeToBed12
 bin/bedpeToVcf
 bin/bgzip
-bin/cnvnator
+bin/cnvnator-multi
 bin/cnvnator2VCF.pl
 bin/cnvnator_wrapper.py
 bin/freebayes
@@ -21,6 +21,43 @@ bin/bwa
 bin/parallel
 bin/sambamba
 bin/variant_effect_predictor.pl
+bin/annotateBed
+bin/bamToBed
+bin/bamToFastq
+bin/bed12ToBed6
+bin/bedToBam
+bin/bedToIgv
+bin/bedpeToBam
+bin/bedtools
+bin/closestBed
+bin/clusterBed
+bin/complementBed
+bin/coverageBed
+bin/expandCols
+bin/fastaFromBed
+bin/flankBed
+bin/genomeCoverageBed
+bin/getOverlap
+bin/groupBy
+bin/intersectBed
+bin/linksBed
+bin/mapBed
+bin/maskFastaFromBed
+bin/mergeBed
+bin/multiBamCov
+bin/multiIntersectBed
+bin/nucBed
+bin/pairToBed
+bin/pairToPair
+bin/randomBed
+bin/shuffleBed
+bin/slopBed
+bin/sortBed
+bin/subtractBed
+bin/tagBam
+bin/unionBedGraphs
+bin/windowBed
+bin/windowMaker
 
 # Compiled source #
 ###################

Makefile

@@ -12,7 +12,7 @@ TABIX_DIR=$(SRC)/tabix
 VAWK_DIR=$(SRC)/vawk
 SVTOOLS_DIR=$(SRC)/svtools
 
-all:	samblaster freebayes lumpy svtyper tabix vawk svtools cnvnator
+all:	samblaster freebayes lumpy svtyper tabix vawk svtools cnvnator-multi
 
 samblaster:
 	$(MAKE) -C $(SAMBLASTER_DIR)
@@ -30,9 +30,9 @@ lumpy:
 svtyper:
 	cp $(SVTYPER_DIR)/svtyper $(TARGET_BIN)
 
-cnvnator:
+cnvnator-multi:
 	$(MAKE) -C $(CNVNATOR_DIR)
-	cp $(CNVNATOR_DIR)/bin/cnvnator $(TARGET_BIN)
+	cp $(CNVNATOR_DIR)/bin/cnvnator-multi $(TARGET_BIN)
 	cp $(CNVNATOR_DIR)/bin/cnvnator_wrapper.py $(TARGET_BIN)
 	cp $(CNVNATOR_DIR)/bin/cnvnator2VCF.pl $(TARGET_BIN)
 

bin/speedseq.config

@@ -14,16 +14,16 @@ SAMBLASTER=`which samblaster || true`
 
 # var/somatic
 FREEBAYES=`which freebayes || true`
-VEP="/shared/external_bin/variant_effect_predictor.pl"
-VEP_CACHE_DIR="/shared/external_bin/ensembl-tools-release-75/cache"
+VEP=`which variant_effect_predictor.pl`
+VEP_CACHE_DIR=~/.vep
 
 # sv
 LUMPY=`which lumpy || true`
 PAIREND_DISTRO=`which pairend_distro.py || true`
-BEDPETOVCF=$SPEEDSEQ_HOME/src/sv-tools/bedpeToVcf
-SVTYPER=$SPEEDSEQ_HOME/src/svtyper/svtyper
+BEDPETOVCF=`which bedpeToVcf || true`
+SVTYPER=`which svtyper || true`
 
 # CNVnator 
-CNVNATOR_WRAPPER=$SPEEDSEQ_HOME/src/cnvnator/bin/cnvnator_wrapper.py
-CNVNATOR=$SPEEDSEQ_HOME/src/cnvnator/bin/cnvnator
+CNVNATOR_WRAPPER=`which cnvnator_wrapper.py || true`
+CNVNATOR=`which cnvnator-multi || true`
 CNVNATOR_CHROMS_DIR=/shared/genomes/b37/full/chroms

speedseq_setup.py

@@ -217,6 +217,18 @@ def main(args):
 		vep.install("perl", "ensembl-tools-release-76/scripts/variant_effect_predictor")
 		vep.cp_bin("ensembl-tools-release-76/scripts/variant_effect_predictor/variant_effect_predictor.pl", args.targetbin)
 		vep.cp_bin("Bio", args.targetbin + "/Bio")
+
+	#BEDtools install
+	bedtools = INSTALLER("bedtools", args.quiet)
+	bedtools.check_install("bedtools")
+	if (bedtools.isInstalled):
+		bedtools.get_update()
+	if (bedtools.notInstalled or bedtools.update):
+		url = "https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz"
+		bedtools.download("curl", url)
+		bedtools.unpack("tar")
+		bedtools.install("make", "bedtools2-2.20.1")
+		bedtools.cp_bin("bedtools2-2.20.1/bin/*", args.targetbin)
 
     	# #gemini install
 	# gemini = INSTALLER("gemini", args.quiet)

src/cnvnator/Makefile

@@ -28,14 +28,14 @@ CNVDIR	     = CNVnator_$(VERSION)
 MAINDIR	     = $(TMPDIR)/$(CNVDIR)
 SRCDIR	     = $(MAINDIR)/src
 
-all:	cnvnator
+all:	cnvnator-multi
 
 .PHONY: samtools
 
 samtools:
 	$(MAKE) -C $(SAMDIR)
 
-cnvnator: samtools $(OBJS)
+cnvnator-multi: samtools $(OBJS)
 	@mkdir -p $(BINDIR)
 	$(CXX) -o $(BINDIR)/$@ $(OBJS) $(SAMLIB) $(LIBS) $(ROOTLIBS)