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-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm84
-rw-r--r--gnu/packages/patches/vcflib-use-shared-libraries.patch135
3 files changed, 29 insertions, 191 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index eb28104add..77f1d4a096 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1703,7 +1703,6 @@ dist_patch_DATA = \
%D%/packages/patches/vboot-utils-fix-format-load-address.patch \
%D%/packages/patches/vboot-utils-fix-tests-show-contents.patch \
%D%/packages/patches/vboot-utils-skip-test-workbuf.patch \
- %D%/packages/patches/vcflib-use-shared-libraries.patch \
%D%/packages/patches/vigra-python-compat.patch \
%D%/packages/patches/vinagre-newer-freerdp.patch \
%D%/packages/patches/vinagre-newer-rdp-parameters.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 77150e0dce..bb97b2d313 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14923,32 +14923,44 @@ library automatically handles index file generation and use.")
(define-public vcflib
(package
(name "vcflib")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/vcflib/vcflib/releases/"
- "download/v" version
- "/vcflib-" version "-src.tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vcflib/vcflib")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
- (patches (search-patches "vcflib-use-shared-libraries.patch"))
+ (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh"))
(modules '((guix build utils)))
(snippet
- `(begin
+ '(begin
+ (substitute* "CMakeLists.txt"
+ ((".*fastahack.*") "")
+ ((".*smithwaterman.*") "")
+ (("(pkg_check_modules\\(TABIXPP)" text)
+ (string-append
+ "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
+ "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
+ text))
+ (("\\$\\{TABIXPP_LIBRARIES\\}" text)
+ (string-append "${FASTAHACK_LIBRARIES} "
+ "${SMITHWATERMAN_LIBRARIES} "
+ text)))
(substitute* (find-files "." "\\.(h|c)(pp)?$")
(("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
(("\"convert.h\"") "<smithwaterman/convert.h>")
(("\"disorder.h\"") "<smithwaterman/disorder.h>")
- (("\"tabix.hpp\"") "<tabix.hpp>")
- (("\"Fasta.h\"") "<fastahack/Fasta.h>"))
+ (("Fasta.h") "fastahack/Fasta.h"))
(for-each delete-file-recursively
'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
- "libVCFH" "multichoose" "smithwaterman" "tabixpp"))
+ "libVCFH" "multichoose" "smithwaterman"))
#t))))
- (build-system gnu-build-system)
+ (build-system cmake-build-system)
(inputs
- `(("htslib" ,htslib)
+ `(("bzip2" ,bzip2)
+ ("htslib" ,htslib)
("fastahack" ,fastahack)
("perl" ,perl)
("python" ,python)
@@ -14961,22 +14973,13 @@ library automatically handles index file generation and use.")
;; Submodules.
;; This package builds against the .o files so we need to extract the source.
("filevercmp-src" ,(package-source filevercmp))
+ ("fsom-src" ,(package-source fsom))
("intervaltree-src" ,(package-source intervaltree))
("multichoose-src" ,(package-source multichoose))))
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'set-flags
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* "Makefile"
- (("LDFLAGS =")
- (string-append "LDFLAGS = -Wl,-rpath="
- (assoc-ref outputs "out") "/lib ")))
- (substitute* "filevercmp/Makefile"
- (("-c") "-c -fPIC"))
- #t))
- (delete 'configure)
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
@@ -14989,39 +14992,10 @@ library automatically handles index file generation and use.")
"--strip-components=1"))))))
(and
(unpack "filevercmp-src" "filevercmp")
+ (unpack "fsom-src" "fsom")
(unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")))))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin"))
- (lib (string-append out "/lib")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "bin" ".*"))
- (install-file "libvcflib.so" lib)
- (install-file "libvcflib.a" lib)
- (for-each
- (lambda (file)
- (install-file file (string-append out "/include")))
- (find-files "include" "\\.h(pp)?$"))
- (mkdir-p (string-append lib "/pkgconfig"))
- (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc")
- (lambda _
- (format #t "prefix=~a~@
- exec_prefix=${prefix}~@
- libdir=${exec_prefix}/lib~@
- includedir=${prefix}/include~@
- ~@
- ~@
- Name: libvcflib~@
- Version: ~a~@
- Requires: smithwaterman, fastahack~@
- Description: C++ library for parsing and manipulating VCF files~@
- Libs: -L${libdir} -lvcflib~@
- Cflags: -I${includedir}~%"
- out ,version))))
- #t)))))
+ (unpack "multichoose-src" "multichoose"))
+ #t))))))
(home-page "https://github.com/vcflib/vcflib/")
(synopsis "Library for parsing and manipulating VCF files")
(description "Vcflib provides methods to manipulate and interpret
diff --git a/gnu/packages/patches/vcflib-use-shared-libraries.patch b/gnu/packages/patches/vcflib-use-shared-libraries.patch
deleted file mode 100644
index e198ec663c..0000000000
--- a/gnu/packages/patches/vcflib-use-shared-libraries.patch
+++ /dev/null
@@ -1,135 +0,0 @@
-This patch is a combination of many of the patches from Debian:
-https://sources.debian.org/src/libvcflib/1.0.1+dfsg-3/debian/patches/
-
----
- Makefile | 63 +++++++++++---------------------------------------------
- 1 file changed, 12 insertions(+), 51 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 6b13350..be85f22 100644
---- a/Makefile
-+++ b/Makefile
-@@ -114,43 +114,25 @@ BIN_SOURCES = src/vcfecho.cpp \
- src/vcfnull2ref.cpp \
- src/vcfinfosummarize.cpp
-
--# when we can figure out how to build on mac
--# src/vcfsom.cpp
--
- #BINS = $(BIN_SOURCES:.cpp=)
- BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
- SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-
--TABIX = tabixpp/tabix.o
--FASTAHACK = fastahack/Fasta.o
--SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
--REPEATS = smithwaterman/Repeats.o
--INDELALLELE = smithwaterman/IndelAllele.o
--DISORDER = smithwaterman/disorder.o
--LEFTALIGN = smithwaterman/LeftAlign.o
--FSOM = fsom/fsom.o
- FILEVERCMP = filevercmp/filevercmp.o
-
--# Work out how to find htslib
--# Use the one we ship in tabixpp unless told otherwise by the environment
--HTS_LIB ?= $(VCF_LIB_LOCAL)/tabixpp/htslib/libhts.a
--HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabixpp/htslib
--HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
--
--
--INCLUDES = $(HTS_INCLUDES) -I$(INC_DIR)
--LDFLAGS = -L$(LIB_DIR) -lvcflib $(HTS_LDFLAGS) -lpthread -lz -lm -llzma -lbz2
-+INCLUDES = -I$(INC_DIR) $(shell pkg-config --cflags htslib fastahack smithwaterman tabixpp)
-+LDFLAGS = -L$(LIB_DIR) -lvcflib -lpthread -lz -lstdc++ -lm -llzma -lbz2 $(shell pkg-config --libs htslib fastahack smithwaterman tabixpp)
-
-
-
--all: $(OBJECTS) $(BINS) scriptToBin
-+all: $(OBJECTS) $(BINS) scriptToBin libvcflib.a
-
- scriptToBin: $(BINS)
- $(CP) scripts/* $(BIN_DIR)
-
- GIT_VERSION += $(shell git describe --abbrev=4 --dirty --always)
-
--CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x
-+CXXFLAGS = -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -fPIC
- #CXXFLAGS = -O2
- #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-@@ -168,7 +150,7 @@ profiling:
- gprof:
- $(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
--$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
-+$(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(FILEVERCMP)
- $(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && $(CP) src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
- multichoose: pre
-@@ -177,39 +159,22 @@ multichoose: pre
- intervaltree: pre
- cd intervaltree && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
--$(TABIX): pre
-- cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
--
--$(SMITHWATERMAN): pre
-- cd smithwaterman && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
--
--$(DISORDER): $(SMITHWATERMAN)
--
--$(REPEATS): $(SMITHWATERMAN)
--
--$(LEFTALIGN): $(SMITHWATERMAN)
--
--$(INDELALLELE): $(SMITHWATERMAN)
--
--$(FASTAHACK): pre
-- cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
--
--#$(FSOM):
--# cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
--
- $(FILEVERCMP): pre
- cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
- $(SHORTBINS): pre
- $(MAKE) $(BIN_DIR)/$@
-
--$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-+$(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP) pre intervaltree
- $(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
-
--libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
-- ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-+libvcflib.a: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+ ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
- $(CP) libvcflib.a $(LIB_DIR)
-
-+libvcflib.so: $(OBJECTS) $(SSW) $(FILEVERCMP) pre
-+ $(CXX) -shared -o libvcflib.so $(OBJECTS) $(SSW) $(FILEVERCMP)
-+ $(CP) libvcflib.so $(LIB_DIR)
-
- test: $(BINS)
- @prove -Itests/lib -w tests/*.t
-@@ -230,16 +195,12 @@ clean:
- $(RM) $(BINS) $(OBJECTS)
- $(RM) ssw_cpp.o ssw.o
- $(RM) libvcflib.a
-+ $(RM) libvcflib.so
- $(RM) -r $(BIN_DIR)
- $(RM) -r $(LIB_DIR)
- $(RM) -r $(INC_DIR)
- $(RM) -r $(OBJ_DIR)
-- $(MAKE) clean -C tabixpp
-- $(MAKE) clean -C smithwaterman
-- $(MAKE) clean -C fastahack
- $(MAKE) clean -C multichoose
-- $(MAKE) clean -C fsom
-- $(MAKE) clean -C libVCFH
- $(MAKE) clean -C test
- $(MAKE) clean -C filevercmp
- $(MAKE) clean -C intervaltree
---
-2.28.0
-