# HG changeset patch # User malbuquerque # Date 1421792962 18000 # Node ID b0c2893ac2a11a25ed7c0e65a6f7ffc594a79900 # Parent 12d6088c8ee6c06088e369fed8ce15e34db812fa Uploaded diff -r 12d6088c8ee6 -r b0c2893ac2a1 Makefile --- a/Makefile Tue Jan 20 17:20:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -DEBUG ?= 0 -PARALLEL ?= 0 - -# External Libraries -BOOST_ROOT ?= /g/solexa/bin/software/boost_1_53_0/ -BAMTOOLS_ROOT ?= /g/solexa/bin/software/bamtools-2.3.0/ -SEQTK_ROOT ?= /g/solexa/bin/software/kseq/ - -# Flags -CXX=g++ -CXXFLAGS += -isystem ${BOOST_ROOT}/include -isystem ${BAMTOOLS_ROOT}/include -isystem ${SEQTK_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -LDFLAGS += -L${BOOST_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -L${BAMTOOLS_ROOT}/lib -lbamtools -lz -Wl,-rpath,${BAMTOOLS_ROOT}/lib,-rpath,${BOOST_ROOT}/lib - -# Additional flags for release/debug -ifeq (${PARALLEL}, 1) - CXXFLAGS += -fopenmp -DOPENMP -else - CXXFLAGS += -DNOPENMP -endif - -# Additional flags for release/debug -ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -else ifeq (${DEBUG}, 2) - CXXFLAGS += -g -O0 -fno-inline -DPROFILE - LDFLAGS += -lprofiler -ltcmalloc -else - CXXFLAGS += -O9 -DNDEBUG - #LDFLAGS += --static -endif - -# External sources -HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h) -BAMTOOLSSOURCES = $(wildcard src/bamtools/src/api/*.h) $(wildcard src/bamtools/src/api/*.cpp) -DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - -# Targets -TARGETS = src/delly src/extract src/cov src/iover src/stats - -all: $(TARGETS) - -src/delly: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - -src/extract: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - -src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - -src/iover: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - -src/stats: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - -clean: - rm -f $(TARGETS) $(TARGETS:=.o) diff -r 12d6088c8ee6 -r b0c2893ac2a1 delly.xml --- a/delly.xml Tue Jan 20 17:20:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ - - - structural variant discovery by integrated paired-end and split-read analysis - - - delly - DELLY_DIR - - - - - - - #for $i, $s in enumerate( $repeatBam ) - ln -s $s.sortedBam ./input$(i).bam; - ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai; - #end for - - - #if not isinstance( $type.value, list ): - #set $args = [ $type.value ] - #else: - #set $args = $type.value - #end if - - - #for $option in $args - - - \$DELLY_DIR/src/delly -t $option -o ./output.$(option).vcf -q $mapQual -s $madCutoff - #if $option == "DEL" - -m $minFlank - #end if - -u $genoQual -v $vcfgeno -g $genome - - - #for $i, $s in enumerate( $repeatBam ) - ./input$(i).bam - #end for - ; - #end for - - - #set $option = $args[0] - grep ^\# output.$(option).vcf > $outfile; - grep ^\# -v output.$(option).vcf > variants.txt; - - - #if isinstance( $type.value, list ): - #for $option in $args[1:] - grep ^\# -v output.$(option).vcf >> variants.txt; - #end for - #end if - - - - sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt; - - - #if $filterCalls - awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile; - #else - cat sortedVariants.txt >> $outfile; - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 12d6088c8ee6 -r b0c2893ac2a1 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 20 17:20:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ - - - - - - - - - - - - - - - - - - - https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz - ls - ls $REPOSITORY_INSTALL_DIR - - ./Makefile - ./badbadbad - - - $REPOSITORY_INSTALL_DIR/Makefile - . - - make all BOOST_ROOT=\$BOOST_ROOT BAMTOOLS_ROOT=\$BAMTOOLS_ROOT SEQTK_ROOT=\$SEQTK_ROOT - - . - $INSTALL_DIR - - - $INSTALL_DIR - - - - - -