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-rw-r--r--gn/packages/bioinformatics.scm49
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