fdc306879b
* gnu/packages/bioinformatics.scm (delly): New variable. * gnu/packages/patches/delly-use-system-libraries.patch: New file. * gnu/local.mk: Include delly-use-system-libraries.patch. Signed-off-by: Leo Famulari <leo@famulari.name>
56 lines
2.1 KiB
Diff
56 lines
2.1 KiB
Diff
--- a/Makefile 2017-04-09 12:48:15.000000000 +0200
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+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200
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@@ -9,8 +9,8 @@
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# Flags
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CXX=g++
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-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
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-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
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+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
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+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
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# Additional flags for release/debug
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ifeq (${PARALLEL}, 1)
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@@ -23,7 +23,7 @@
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ifeq (${STATIC}, 1)
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LDFLAGS += -static -static-libgcc -pthread -lhts -lz
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else
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- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
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+ LDFLAGS += -lhts -lz
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endif
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ifeq (${DEBUG}, 1)
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CXXFLAGS += -g -O0 -fno-inline -DDEBUG
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@@ -41,29 +41,17 @@
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DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
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# Targets
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-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe
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+TARGETS = src/delly src/cov src/dpe
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all: $(TARGETS)
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-.htslib: $(HTSLIBSOURCES)
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- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
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-
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-.bcftools: $(HTSLIBSOURCES)
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- cd src/bcftools && make && cd ../../ && touch .bcftools
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-
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-.boost: $(BOOSTSOURCES)
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- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
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-
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-src/delly: .htslib .bcftools .boost $(DELLYSOURCES)
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- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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-
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-src/cov: .htslib .bcftools .boost $(DELLYSOURCES)
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+src/cov: $(DELLYSOURCES)
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$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES)
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+src/dpe: $(DELLYSOURCES)
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$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
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clean:
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cd src/htslib && make clean
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cd src/modular-boost && ./b2 --clean-all
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- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools
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+ rm -f $(TARGETS) $(TARGETS:=.o)
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