diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 49 |
1 files changed, 43 insertions, 6 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4f802f7..700dec4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2268,7 +2268,7 @@ in-memory footprint at the cost of packing and unpacking.") (substitute* "Makefile" ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. (("cairo libzstd") - "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack") + "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate") ;; Skip the part where we link static libraries special. It doesn't like the changes we make (("-Wl,-B.*") "\n") @@ -2285,6 +2285,10 @@ in-memory footprint at the cost of packing and unpacking.") (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") (string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc")) + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") + ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") + (string-append " " (assoc-ref inputs "libdeflate") "/lib/libdeflate.so")) + ((" \\$\\(LIB_DIR\\)/libvcflib.a") (string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) ((" \\$\\(BIN_DIR\\)/vcf2tsv") @@ -2309,8 +2313,12 @@ in-memory footprint at the cost of packing and unpacking.") ;((" \\$\\(LIB_DIR\\)/libsdsl.a") ; (string-append " " (assoc-ref inputs "sdsl-lite") "/lib/libsdsl.so")) + ((" \\$\\(LIB_DIR\\)/%divsufsort.a") + (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so")) + ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") + (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort64.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so")) @@ -2325,10 +2333,38 @@ in-memory footprint at the cost of packing and unpacking.") ((" \\$\\(LIB_DIR\\)/libraptor2.a") (string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so")) ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))) - ;; vcf2tsv shows up in a couple of other places - (substitute* "test/t/02_vg_construct.t" - (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))))) + (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))))) + #; + (add-before 'patch-source 'use-shared-libvg + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "Makefile" + (("libvg\\.a") "libvg.so") + ;; Have the linker find the shared library. + (("\\$\\(LIB_DIR\\)/libvg.\\$\\(SHARED_SUFFIX\\) \\$\\(LDFLAGS\\)") + "-lvg $(LDFLAGS)") + (("\\$\\(LDFLAGS\\) \\$\\(LIB_DIR\\)/libvg.so") + "$(LDFLAGS) -lvg")) + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" + (assoc-ref outputs "out") "/lib")) + + ;; We need to tell a number of dependencies to build with -fPIC. + (substitute* "Makefile" + (("^CXXFLAGS := -O3") + (string-append "CFLAGS := -fPIC\n" + "CXXFLAGS := -O3 -fPIC")) + (("^export CXXFLAGS") + (string-append "export CFLAGS\n" + "$(info CFLAGS are $(CFLAGS))\n" + "export CXXFLAGS")) + ((" \\$\\(LIB_DIR\\)/libjemalloc.a") + (string-append " " (assoc-ref inputs "jemalloc") + "/lib/libjemalloc_pic.a"))) + ;; We don't want to pull in all the global CXXFLAGS here. + (substitute* "deps/sublinear-Li-Stephens/makefile" + (("^CXXFLAGS:=") "CXXFLAGS:= -fPIC ")) + ;; CMAKE_CXX_FLAGS aren't set globally. + (substitute* "deps/kff-cpp-api/CMakeLists.txt" + (("CMAKE_CXX_FLAGS \"") "CMAKE_CXX_FLAGS \" -fPIC ")))) (add-after 'unpack 'dont-build-shared-vgio (lambda _ ;; vg will link with libvgio and fail the 'validate-runpath phase. @@ -2378,7 +2414,7 @@ in-memory footprint at the cost of packing and unpacking.") (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (install-file "bin/vg" (string-append out "/bin")) - (install-file "lib/libvg.a" (string-append out "/lib")) + ;(install-file "lib/libvg.so" (string-append out "/lib")) (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) @@ -2408,6 +2444,7 @@ in-memory footprint at the cost of packing and unpacking.") htslib jansson jemalloc + libdeflate libdivsufsort ncurses openmpi |