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Makefile
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VERSION=0.0.1
TARGET_BIN=bin
SRC=src
SPEEDSEQ_DIR=$(shell pwd)
BWA_DIR=$(SRC)/bwa
SAMBLASTER_DIR=$(SRC)/samblaster
FREEBAYES_DIR=$(SRC)/freebayes
LUMPY_DIR=$(SRC)/lumpy-sv
SVTYPER_DIR=$(SRC)/svtyper
CNVNATOR_DIR=$(SRC)/cnvnator
TABIX_DIR=$(SRC)/tabix
VAWK_DIR=$(SRC)/vawk
SVTOOLS_DIR=$(SRC)/svtools
MBUFFER_DIR=$(SRC)/mbuffer
SCRIPTS_DIR=$(SRC)/scripts
all: bwa samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer scripts cnvnator-multi
bwa:
$(MAKE) -C $(BWA_DIR)
cp $(BWA_DIR)/bwa $(TARGET_BIN)
samblaster:
$(MAKE) -C $(SAMBLASTER_DIR)
cp $(SAMBLASTER_DIR)/samblaster $(TARGET_BIN)
freebayes:
$(MAKE) -C $(FREEBAYES_DIR)
cp $(FREEBAYES_DIR)/bin/freebayes $(TARGET_BIN)
lumpy:
$(MAKE) -C $(LUMPY_DIR)
cp $(LUMPY_DIR)/scripts/pairend_distro.py $(TARGET_BIN)
cp $(LUMPY_DIR)/bin/lumpy $(TARGET_BIN)
svtyper:
cp $(SVTYPER_DIR)/svtyper $(TARGET_BIN)
cnvnator-multi:
ifeq ($(ROOTSYS),)
@echo -e "\nWARNING: CNVnator not compiled because the ROOT package is not installed."
@echo "Please see the README for instructions on manually installing ROOT."
else
$(MAKE) -C $(CNVNATOR_DIR)
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)
cp $(CNVNATOR_DIR)/bin/annotate_rd.py $(TARGET_BIN)
endif
tabix:
$(MAKE) -C $(TABIX_DIR)
cp $(TABIX_DIR)/tabix $(TARGET_BIN)
cp $(TABIX_DIR)/bgzip $(TARGET_BIN)
vawk:
cp $(VAWK_DIR)/vawk $(TARGET_BIN)
svtools:
cp $(SVTOOLS_DIR)/bedpeToBed12 $(TARGET_BIN)
cp $(SVTOOLS_DIR)/bedpeToVcf $(TARGET_BIN)
cp $(SVTOOLS_DIR)/splitReadSamToBedpe $(TARGET_BIN)
cp $(SVTOOLS_DIR)/splitterToBreakpoint $(TARGET_BIN)
cp $(SVTOOLS_DIR)/vcfToBedpe $(TARGET_BIN)
cp $(SVTOOLS_DIR)/lumpyToBedpe $(TARGET_BIN)
mbuffer:
cd $(MBUFFER_DIR); ./configure --prefix=$(shell pwd)
$(MAKE) -C $(MBUFFER_DIR)
cp $(MBUFFER_DIR)/mbuffer $(TARGET_BIN)
scripts:
cp $(SCRIPTS_DIR)/bamtofastq.py $(TARGET_BIN)
cp $(SCRIPTS_DIR)/bamheadrg.py $(TARGET_BIN)
cp $(SCRIPTS_DIR)/bamgroupreads.py $(TARGET_BIN)
cp $(SCRIPTS_DIR)/bamfilterrg.py $(TARGET_BIN)
clean:
rm -f bin/bedpeToBed12 bin/bedpeToVcf bin/bgzip bin/cnvnator bin/cnvnator2VCF.pl bin/cnvnator_wrapper.py bin/freebayes bin/lumpy bin/pairend_distro.py bin/samblaster bin/splitReadSamToBedpe bin/splitterToBreakpoint bin/svtyper bin/tabix bin/vawk bin/vcfToBedpe
$(MAKE) -C $(BWA_DIR) clean
$(MAKE) -C $(SAMBLASTER_DIR) clean
$(MAKE) -C $(FREEBAYES_DIR) clean
$(MAKE) -C $(LUMPY_DIR) clean
$(MAKE) -C $(CNVNATOR_DIR) clean
$(MAKE) -C $(LUMPY_DIR) clean
$(MAKE) -C $(TABIX_DIR) clean
$(MAKE) -C $(MBUFFER_DIR) clean