gnu: vcflib: Use shared libraries.

* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

gnu/local.mk

@@ -1639,6 +1639,7 @@ 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

@@ -15641,9 +15641,16 @@ (define-public vcflib
                            "/vcflib-" version "-src.tar.gz"))
        (sha256
         (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+       (patches (search-patches "vcflib-use-shared-libraries.patch"))
        (modules '((guix build utils)))
        (snippet
         `(begin
+           (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>"))
            (for-each delete-file-recursively
                      '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
                        "libVCFH" "multichoose" "smithwaterman" "tabixpp"))
@@ -15651,34 +15658,34 @@ (define-public vcflib
     (build-system gnu-build-system)
     (inputs
      `(("htslib" ,htslib)
+       ("fastahack" ,fastahack)
        ("perl" ,perl)
        ("python" ,python)
+       ("smithwaterman" ,smithwaterman)
+       ("tabixpp" ,tabixpp)
+       ("xz" ,xz)
        ("zlib" ,zlib)))
     (native-inputs
-     `(;; Submodules.
+     `(("pkg-config" ,pkg-config)
+       ;; Submodules.
        ;; This package builds against the .o files so we need to extract the source.
-       ("fastahack-src" ,(package-source fastahack))
        ("filevercmp-src" ,(package-source filevercmp))
-       ("fsom-src" ,(package-source fsom))
        ("intervaltree-src" ,(package-source intervaltree))
-       ("multichoose-src" ,(package-source multichoose))
-       ("smithwaterman-src" ,(package-source smithwaterman))
-       ("tabixpp-src" ,(package-source tabixpp))))
+       ("multichoose-src" ,(package-source multichoose))))
     (arguments
      `(#:tests? #f ; no tests
-       #:make-flags (list (string-append "HTS_LIB="
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/lib/libhts.a")
-                          (string-append "HTS_INCLUDES= -I"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib")
-                          (string-append "HTS_LDFLAGS= -L"
-                                         (assoc-ref %build-inputs "htslib")
-                                         "/include/htslib" " -lhts"))
        #: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)
-         (delete 'check)
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((unpack (lambda (source target)
@@ -15690,34 +15697,23 @@ (define-public vcflib
                                            (assoc-ref inputs source)
                                            "--strip-components=1"))))))
                (and
-                (unpack "fastahack-src" "fastahack")
                 (unpack "filevercmp-src" "filevercmp")
-                (unpack "fsom-src" "fsom")
                 (unpack "intervaltree-src" "intervaltree")
-                (unpack "multichoose-src" "multichoose")
-                (unpack "smithwaterman-src" "smithwaterman")
-                (unpack "tabixpp-src" "tabixpp")))))
-         (replace 'build
-           (lambda* (#:key inputs make-flags #:allow-other-keys)
-             (let ((htslib (assoc-ref inputs "htslib")))
-               (with-directory-excursion "tabixpp"
-                 (substitute* "Makefile"
-                   (("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
-                   (("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
-                   (("htslib/htslib") (string-append htslib "/include/htslib")))
-                 (invoke "make"
-                         (string-append "HTS_LIB=" htslib "/lib/libhts.a")))
-               (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
+                (unpack "multichoose-src" "multichoose")))))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                   (lib (string-append (assoc-ref outputs "out") "/lib")))
+             (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" ".*"))
-               ;; The header files in src/ do not interface libvcflib,
-               ;; therefore they are left out.
-               (install-file "libvcflib.a" lib))
+               (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)?$")))
              #t)))))
     (home-page "https://github.com/vcflib/vcflib/")
     (synopsis "Library for parsing and manipulating VCF files")

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

@@ -0,0 +1,135 @@
+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
+