diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 36 |
1 files changed, 0 insertions, 36 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 397b38f..e0586fb 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2403,10 +2403,6 @@ in-memory footprint at the cost of packing and unpacking.") ((" \\$\\(LIB_DIR\\)/libdw.a") (string-append " " (search-input-file inputs "/lib/libdw.so"))) - ;; We need the Make.helper file in SDSL_DIR for gcsa2 - ;((" \\$\\(LIB_DIR\\)/libsdsl.a") - ; (string-append " " (search-input-file inputs "/lib/libsdsl.so"))) - ((" \\$\\(LIB_DIR\\)/%divsufsort.a") (string-append " " (dirname (search-input-file inputs "/lib/libdivsufsort.so")) @@ -2445,37 +2441,6 @@ in-memory footprint at the cost of packing and unpacking.") (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") (dirname (search-input-file inputs "/include/divsufsort.h")))))) - #; - (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. @@ -2529,7 +2494,6 @@ 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.so" (string-append out "/lib")) (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) |