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authorRoel Janssen <roel@gnu.org>2018-03-29 14:58:15 +0200
committerLeo Famulari <leo@famulari.name>2018-03-30 10:48:01 -0400
commitfdc306879b388b08be63ead6209473c184daa1e0 (patch)
treea7e7e2e8f0fadaf0b49993d550416157af11c4a6 /gnu/packages
parent183ce9884924794677eefca78cf445ada5551260 (diff)
downloadguix-fdc306879b388b08be63ead6209473c184daa1e0.tar
guix-fdc306879b388b08be63ead6209473c184daa1e0.tar.gz
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>
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm47
-rw-r--r--gnu/packages/patches/delly-use-system-libraries.patch56
2 files changed, 103 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index af515c026e..66d5bd3707 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2030,6 +2030,53 @@ normalized and standardized files, multiple visualizations can be created to
identify enrichments with functional annotations of the genome.")
(license license:gpl3+)))
+(define-public delly
+ (package
+ (name "delly")
+ (version "0.7.7")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/tobiasrausch/delly/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
+ (patches (search-patches "delly-use-system-libraries.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
+ (templates (string-append (assoc-ref %outputs "out")
+ "/share/delly/templates")))
+ (mkdir-p bin)
+ (mkdir-p templates)
+ (copy-recursively "excludeTemplates" templates)
+ (install-file "src/cov" bin)
+ (install-file "src/delly" bin)
+ (install-file "src/dpe" bin)))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (inputs
+ `(("boost" ,boost)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("bzip2" ,bzip2)))
+ (home-page "https://github.com/tobiasrausch/delly")
+ (synopsis "Integrated structural variant prediction method")
+ (description "Delly is an integrated structural variant prediction method
+that can discover and genotype deletions, tandem duplications, inversions and
+translocations at single-nucleotide resolution in short-read massively parallel
+sequencing data. It uses paired-ends and split-reads to sensitively and
+accurately delineate genomic rearrangements throughout the genome.")
+ (license license:gpl3+)))
+
(define-public diamond
(package
(name "diamond")
diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch
new file mode 100644
index 0000000000..3315c2a176
--- /dev/null
+++ b/gnu/packages/patches/delly-use-system-libraries.patch
@@ -0,0 +1,56 @@
+--- a/Makefile 2017-04-09 12:48:15.000000000 +0200
++++ b/Makefile 2017-06-21 14:26:02.749282787 +0200
+@@ -9,8 +9,8 @@
+
+ # Flags
+ CXX=g++
+-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
+-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
++CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
++LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
+
+ # Additional flags for release/debug
+ ifeq (${PARALLEL}, 1)
+@@ -23,7 +23,7 @@
+ ifeq (${STATIC}, 1)
+ LDFLAGS += -static -static-libgcc -pthread -lhts -lz
+ else
+- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
++ LDFLAGS += -lhts -lz
+ endif
+ ifeq (${DEBUG}, 1)
+ CXXFLAGS += -g -O0 -fno-inline -DDEBUG
+@@ -41,29 +41,17 @@
+ DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
+
+ # Targets
+-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe
++TARGETS = src/delly src/cov src/dpe
+
+ all: $(TARGETS)
+
+-.htslib: $(HTSLIBSOURCES)
+- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
+-
+-.bcftools: $(HTSLIBSOURCES)
+- cd src/bcftools && make && cd ../../ && touch .bcftools
+-
+-.boost: $(BOOSTSOURCES)
+- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
+-
+-src/delly: .htslib .bcftools .boost $(DELLYSOURCES)
+- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+-
+-src/cov: .htslib .bcftools .boost $(DELLYSOURCES)
++src/cov: $(DELLYSOURCES)
+ $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES)
++src/dpe: $(DELLYSOURCES)
+ $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+ clean:
+ cd src/htslib && make clean
+ cd src/modular-boost && ./b2 --clean-all
+- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools
++ rm -f $(TARGETS) $(TARGETS:=.o)