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authorRicardo Wurmus <rekado@elephly.net>2018-10-21 14:00:07 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-10-21 23:06:46 +0200
commit7a1e62ca67849f9ca19ded4d26c542021db71e38 (patch)
tree0b2d20288c9988592bb6fa9a6e1e027a048bc80c /gnu
parent4d494a4fa3ebb2d1deacede405d0b0d8e5dbc32b (diff)
downloadpatches-7a1e62ca67849f9ca19ded4d26c542021db71e38.tar
patches-7a1e62ca67849f9ca19ded4d26c542021db71e38.tar.gz
gnu: delly: Update to 0.7.9.
* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm40
-rw-r--r--gnu/packages/patches/delly-use-system-libraries.patch56
3 files changed, 20 insertions, 77 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index c76908f92f..d155b4c613 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -642,7 +642,6 @@ dist_patch_DATA = \
%D%/packages/patches/datamash-arm-tests.patch \
%D%/packages/patches/dbus-helper-search-path.patch \
%D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
- %D%/packages/patches/delly-use-system-libraries.patch \
%D%/packages/patches/dfu-programmer-fix-libusb.patch \
%D%/packages/patches/diffutils-gets-undeclared.patch \
%D%/packages/patches/diffutils-getopt.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc21848367..78debbc873 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2155,42 +2155,42 @@ identify enrichments with functional annotations of the genome.")
(define-public delly
(package
(name "delly")
- (version "0.7.7")
+ (version "0.7.9")
(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"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dellytools/delly.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
- (patches (search-patches "delly-use-system-libraries.patch"))))
+ (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/htslib")
+ #t))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests to run.
- #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+ #:make-flags
+ (list "PARALLEL=1" ; Allow parallel execution at run-time.
+ (string-append "prefix=" (assoc-ref %outputs "out")))
#: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")
+ (add-after 'install 'install-templates
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((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)))
+ #t))))))
(inputs
`(("boost" ,boost)
("htslib" ,htslib)
("zlib" ,zlib)
("bzip2" ,bzip2)))
- (home-page "https://github.com/tobiasrausch/delly")
+ (home-page "https://github.com/dellytools/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
diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch
deleted file mode 100644
index 3315c2a176..0000000000
--- a/gnu/packages/patches/delly-use-system-libraries.patch
+++ /dev/null
@@ -1,56 +0,0 @@
---- 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)