gnu: vcflib: Update to 1.0.2.

* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2.
[source]: Download using git-fetch. Remove patch. Update snippet to use
packaged libraries.
[build-system]: Switch to cmake-build-system.
[inputs]: Add bzip2.
[native-inputs]: Add package-source of fsom.
[arguments]: Delete custom 'set-flags, 'install phases. Don't delete
'configure phase. Adjust 'unpack-submodule-sources phase.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

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      \

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)
+       (method git-fetch)
-       (uri (string-append "https://github.com/vcflib/vcflib/releases/"
+       (uri (git-reference
-                           "download/v" version
+              (url "https://github.com/vcflib/vcflib")
-                           "/vcflib-" version "-src.tar.gz"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+        (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh"))
-       (patches (search-patches "vcflib-use-shared-libraries.patch"))
        (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")))))
+                (unpack "multichoose-src" "multichoose"))
-         (replace 'install
+               #t))))))
-           (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)))))
     (home-page "https://github.com/vcflib/vcflib/")
     (synopsis "Library for parsing and manipulating VCF files")
     (description "Vcflib provides methods to manipulate and interpret

gnu/packages/patches/vcflib-use-shared-libraries.patch

@@ -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
-