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.
This commit is contained in:
Ricardo Wurmus 2018-10-21 14:00:07 +02:00
parent 4d494a4fa3
commit 7a1e62ca67
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
3 changed files with 20 additions and 77 deletions

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@ -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 \

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@ -2155,42 +2155,42 @@ (define-public deeptools
(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

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@ -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)