Master

.gitignore

@@ -1,7 +1,5 @@
 # Binaries #
 ############
-bin/bedpeToBed12
-bin/bedpeToVcf
 bin/bgzip
 bin/cnvnator-multi
 src/cnvnator/bin/cnvnator-multi
@@ -13,8 +11,6 @@ bin/lumpy
 bin/lumpyexpress
 bin/pairend_distro.py
 bin/samblaster
-bin/splitReadSamToBedpe
-bin/splitterToBreakpoint
 bin/svtyper
 bin/tabix
 bin/vawk
@@ -65,7 +61,6 @@ bin/mbuffer
 bin/parallel
 bin/bamheadrg.py
 bin/bamtofastq.py
-bin/lumpyToBedpe
 bin/bamgroupreads.py
 bin/bamfilterrg.py
 bin/bamcleanheader.py

.gitmodules

@@ -1,24 +1,18 @@
 [submodule "src/svtyper"]
 	path = src/svtyper
-	url = https://github.com/cc2qe/svtyper.git
+	url = https://github.com/hall-lab/svtyper.git
 [submodule "src/samblaster"]
 	path = src/samblaster
 	url = https://github.com/GregoryFaust/samblaster.git
 [submodule "src/vawk"]
 	path = src/vawk
 	url = https://github.com/cc2qe/vawk.git
-[submodule "src/lumpy-sv"]
-	path = src/lumpy-sv
-	url = https://github.com/cc2qe/lumpy-sv.git
 [submodule "src/tabix"]
 	path = src/tabix
 	url = https://github.com/samtools/tabix.git
 [submodule "src/freebayes"]
 	path = src/freebayes
 	url = https://github.com/ekg/freebayes.git
-[submodule "src/svtools"]
-	path = src/svtools
-	url = https://github.com/hall-lab/sv-tools.git
 [submodule "src/bwa"]
 	path = src/bwa
 	url = https://github.com/lh3/bwa.git
@@ -28,3 +22,10 @@
 [submodule "src/parallel"]
 	path = src/parallel
 	url = http://git.savannah.gnu.org/r/parallel.git
+[submodule "src/lumpy-sv"]
+	path = src/lumpy-sv
+	url = https://github.com/hall-lab/lumpy-sv.git
+	branch = 0.2.13_cram_support
+[submodule "src/CNVnator"]
+	path = src/CNVnator
+	url = https://github.com/abyzovlab/CNVnator

src/cnvnator/src/samtools/COPYING → LICENSE

@@ -1,6 +1,6 @@
-The MIT License
+The MIT License (MIT)
 
-Copyright (c) 2008-2009 Genome Research Ltd.
+Copyright (c) 2014 Ira Hall lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

@@ -9,32 +9,66 @@ SAMBLASTER_DIR=$(SRC)/samblaster
 FREEBAYES_DIR=$(SRC)/freebayes
 LUMPY_DIR=$(SRC)/lumpy-sv
 SVTYPER_DIR=$(SRC)/svtyper
-CNVNATOR_DIR=$(SRC)/cnvnator
+CNVNATOR_DIR=$(SRC)/CNVnator
+SAMTOOLS_VERSION=samtools-1.3.1
+SAMTOOLS_DIR=$(SRC)/$(SAMTOOLS_VERSION)
 TABIX_DIR=$(SRC)/tabix
 VAWK_DIR=$(SRC)/vawk
-SVTOOLS_DIR=$(SRC)/svtools
 MBUFFER_DIR=$(SRC)/mbuffer
 PARALLEL_DIR=$(SRC)/parallel
 BAMKIT_DIR=$(SRC)/bamkit
 
-all:	bwa sambamba samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer parallel bamkit cnvnator-multi
+# all
+all:
+	@echo "" > $(MKFILE_DIR)/install.log
+	@echo "Installing align module..." >> $(MKFILE_DIR)/install.log
+	$(MAKE) align
+	@echo "Done." >> $(MKFILE_DIR)/install.log
 
+	@echo "Installing var and somatic modules..." >> $(MKFILE_DIR)/install.log
+	$(MAKE) var
+	@echo "Done." >> $(MKFILE_DIR)/install.log
+
+	@echo "Installing sv module..." >> $(MKFILE_DIR)/install.log
+	$(MAKE) sv
+	@echo "Done." >> $(MKFILE_DIR)/install.log
+
+	@echo "Installing realign module..." >> $(MKFILE_DIR)/install.log
+	$(MAKE) realign
+	@echo "Done." >> $(MKFILE_DIR)/install.log
+
+	@echo "Installation successful" >> $(MKFILE_DIR)/install.log
+
+# modules
+align: bwa sambamba samblaster parallel config
+
+var: freebayes tabix vawk parallel config
+
+somatic: var
+
+sv: lumpy sambamba samblaster vawk bamkit tabix svtyper cnvnator config
+
+realign: bwa sambamba samblaster parallel mbuffer bamkit config
+
+# autogenerate speedseq.config
+config:
 	@echo "" > $(TARGET_BIN)/speedseq.config
 	@echo "SPEEDSEQ_HOME=$(MKFILE_DIR)" >> $(TARGET_BIN)/speedseq.config
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# general" >> $(TARGET_BIN)/speedseq.config
+	@echo "SAMTOOLS=`which samtools`" >> $(TARGET_BIN)/speedseq.config
 	@echo "SAMBAMBA=$(MKFILE_DIR)/$(TARGET_BIN)/sambamba" >> $(TARGET_BIN)/speedseq.config
 	@echo "BGZIP=$(MKFILE_DIR)/$(TARGET_BIN)/bgzip" >> $(TARGET_BIN)/speedseq.config
 	@echo "TABIX=$(MKFILE_DIR)/$(TARGET_BIN)/tabix" >> $(TARGET_BIN)/speedseq.config
 	@echo "VAWK=$(MKFILE_DIR)/$(TARGET_BIN)/vawk" >> $(TARGET_BIN)/speedseq.config
 	@echo "PARALLEL=$(MKFILE_DIR)/$(TARGET_BIN)/parallel" >> $(TARGET_BIN)/speedseq.config
 	@echo "PYTHON=`which python2.7`" >> $(TARGET_BIN)/speedseq.config
+	@echo "HEXDUMP=`which hexdump`" >> $(TARGET_BIN)/speedseq.config
 
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# align" >> $(TARGET_BIN)/speedseq.config
 	@echo "BWA=$(MKFILE_DIR)/$(TARGET_BIN)/bwa" >> $(TARGET_BIN)/speedseq.config
 	@echo "SAMBLASTER=$(MKFILE_DIR)/$(TARGET_BIN)/samblaster" >> $(TARGET_BIN)/speedseq.config
-	@echo "SAMBAMBA=$(MKFILE_DIR)/$(TARGET_BIN)/sambamba" >> $(TARGET_BIN)/speedseq.config
 
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# var/somatic" >> $(TARGET_BIN)/speedseq.config
@@ -55,9 +89,9 @@ all:	bwa sambamba samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# CNVnator" >> $(TARGET_BIN)/speedseq.config
 	@echo "CNVNATOR_WRAPPER=$(MKFILE_DIR)/$(TARGET_BIN)/cnvnator_wrapper.py" >> $(TARGET_BIN)/speedseq.config
-	@echo "CNVNATOR_MULTI=$(MKFILE_DIR)/$(TARGET_BIN)/cnvnator-multi" >> $(TARGET_BIN)/speedseq.config
-	@echo "ANNOTATE_RD=$(MKFILE_DIR)/$(TARGET_BIN)/annotate_rd" >> $(TARGET_BIN)/speedseq.config
-	@echo "CNVNATOR_CHROMS_DIR=" >> $(TARGET_BIN)/speedseq.config
+	@echo "CNVNATOR=$(MKFILE_DIR)/$(TARGET_BIN)/cnvnator" >> $(TARGET_BIN)/speedseq.config
+	@echo "ANNOTATE_RD=$(MKFILE_DIR)/$(TARGET_BIN)/annotate_rd.py" >> $(TARGET_BIN)/speedseq.config
+	@echo "CNVNATOR_CHROMS_DIR=$(MKFILE_DIR)/$(ANNOTATIONS_DIR)/cnvnator_chroms" >> $(TARGET_BIN)/speedseq.config
 
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# realign" >> $(TARGET_BIN)/speedseq.config
@@ -66,6 +100,7 @@ all:	bwa sambamba samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer
 	@echo "BAMHEADRG=$(MKFILE_DIR)/$(TARGET_BIN)/bamheadrg.py" >> $(TARGET_BIN)/speedseq.config
 	@echo "BAMCLEANHEADER=$(MKFILE_DIR)/$(TARGET_BIN)/bamcleanheader.py" >> $(TARGET_BIN)/speedseq.config
 
+# applications
 bwa:
 	$(MAKE) -C $(BWA_DIR)
 	cp $(BWA_DIR)/bwa $(TARGET_BIN)
@@ -86,20 +121,23 @@ lumpy:
 	cp $(LUMPY_DIR)/scripts/pairend_distro.py $(TARGET_BIN)
 	cp $(LUMPY_DIR)/bin/lumpy $(TARGET_BIN)
 	cp $(LUMPY_DIR)/bin/lumpyexpress $(TARGET_BIN)
+	cp $(LUMPY_DIR)/scripts/vcfToBedpe $(TARGET_BIN)
 
 svtyper:
 	cp $(SVTYPER_DIR)/svtyper $(TARGET_BIN)
 
-cnvnator-multi:
+samtools:
+	cd $(SAMTOOLS_DIR) && ./configure
+	$(MAKE) -C $(SAMTOOLS_DIR)
+
+cnvnator: samtools
 ifeq ($(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
+	ln -f -s ../$(SAMTOOLS_VERSION) -T $(CNVNATOR_DIR)/samtools
 	$(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)
+	cp $(CNVNATOR_DIR)/cnvnator $(TARGET_BIN)
 endif
 
 tabix:
@@ -110,14 +148,6 @@ tabix:
 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)
@@ -138,36 +168,31 @@ bamkit:
 
 clean:
 	rm -f \
-		bin/bedpeToBed12 \
-		bin/bedpeToVcf \
 		bin/bgzip \
 		bin/sambamba \
 		bin/cnvnator \
 		bin/cnvnator2VCF.pl \
 		bin/cnvnator_wrapper.py \
+		bin/annotate_rd.py \
 		bin/freebayes \
 		bin/lumpy \
 		bin/lumpyexpress \
 		bin/pairend_distro.py \
 		bin/samblaster \
-		bin/splitReadSamToBedpe \
-		bin/splitterToBreakpoint \
 		bin/svtyper \
 		bin/tabix \
 		bin/vawk \
 		bin/vcfToBedpe \
 		bin/bwa \
-		bin/lumpyToBedpe \
 		bin/mbuffer \
 		bin/parallel \
 		bin/bamtofastq.py \
 		bin/bamheadrg.py \
 		bin/bamgroupreads.py \
 		bin/bamfilterrg.py \
 		bin/bamcleanheader.py \
-		bin/bamlibs.py \
-		bin/cnvnator-multi \
-		bin/annotate_rd.py
+		bin/bamlibs.py
+
 	$(MAKE) -C $(BWA_DIR) clean
 	$(MAKE) -C $(SAMBLASTER_DIR) clean
 	$(MAKE) -C $(FREEBAYES_DIR) clean