# 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
-
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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 @@
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- https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz
- ls
- ls $REPOSITORY_INSTALL_DIR
-
-
- ./badbadbad
-
-
-
- .
-
- make all BOOST_ROOT=\$BOOST_ROOT BAMTOOLS_ROOT=\$BAMTOOLS_ROOT SEQTK_ROOT=\$SEQTK_ROOT
-
- .
- $INSTALL_DIR
-
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- $INSTALL_DIR
-
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-