# HG changeset patch
# User malbuquerque
# Date 1421800591 18000
# Node ID 1e5b1f1b46c1a23ad14b43972cc36f8e059ee667
# Parent a9a4557de9ca1e94a5e0b41a303d27765a29b262
Uploaded
diff -r a9a4557de9ca -r 1e5b1f1b46c1 Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile Tue Jan 20 19:36:31 2015 -0500
@@ -0,0 +1,58 @@
+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 a9a4557de9ca -r 1e5b1f1b46c1 delly.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/delly.xml Tue Jan 20 19:36:31 2015 -0500
@@ -0,0 +1,106 @@
+
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+ structural variant discovery by integrated paired-end and split-read analysis
+
+
+ delly
+ DELLY_DIR
+
+
+
+
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+
+ #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
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diff -r a9a4557de9ca -r 1e5b1f1b46c1 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Jan 20 19:36:31 2015 -0500
@@ -0,0 +1,53 @@
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+ https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz
+ pwd > ~/delly.pwd.txt
+ echo $INSTALL_DIR > ~/delly.dir.txt
+ sleep 25
+ make -f $REPOSITORY_INSTALL_DIR/Makefile all BOOST_ROOT=$BOOST_ROOT_DIR/ BAMTOOLS_ROOT=$BAMTOOLS_ROOT/ SEQTK_ROOT=$SEQTK_ROOT/
+
+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR
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