gnu: Add delly.
* 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>
This commit is contained in:
Roel Janssen
Leo Famulari
parent
183ce98849
commit
fdc306879b
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@ -621,6 +621,7 @@ dist_patch_DATA = \
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%D%/packages/patches/cyrus-sasl-CVE-2013-4122.patch \
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%D%/packages/patches/dbus-helper-search-path.patch \
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%D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
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%D%/packages/patches/delly-use-system-libraries.patch \
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%D%/packages/patches/dfu-programmer-fix-libusb.patch \
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%D%/packages/patches/diffutils-gets-undeclared.patch \
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%D%/packages/patches/diffutils-getopt.patch \
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@ -2030,6 +2030,53 @@ normalized and standardized files, multiple visualizations can be created to
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identify enrichments with functional annotations of the genome.")
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(license license:gpl3+)))
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(define-public delly
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(package
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(name "delly")
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(version "0.7.7")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/tobiasrausch/delly/archive/v"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
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(patches (search-patches "delly-use-system-libraries.patch"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; There are no tests to run.
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#:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
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#:phases
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(modify-phases %standard-phases
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(delete 'configure) ; There is no configure phase.
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(replace 'install
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(lambda _
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(let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
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(templates (string-append (assoc-ref %outputs "out")
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"/share/delly/templates")))
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(mkdir-p bin)
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(mkdir-p templates)
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(copy-recursively "excludeTemplates" templates)
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(install-file "src/cov" bin)
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(install-file "src/delly" bin)
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(install-file "src/dpe" bin)))))))
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(native-inputs
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`(("python" ,python-2)))
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(inputs
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`(("boost" ,boost)
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("htslib" ,htslib)
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("zlib" ,zlib)
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("bzip2" ,bzip2)))
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(home-page "https://github.com/tobiasrausch/delly")
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(synopsis "Integrated structural variant prediction method")
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(description "Delly is an integrated structural variant prediction method
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that can discover and genotype deletions, tandem duplications, inversions and
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translocations at single-nucleotide resolution in short-read massively parallel
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sequencing data. It uses paired-ends and split-reads to sensitively and
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accurately delineate genomic rearrangements throughout the genome.")
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(license license:gpl3+)))
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(define-public diamond
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(package
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(name "diamond")
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@ -0,0 +1,56 @@
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--- 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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