diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 21 |
1 files changed, 18 insertions, 3 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6c8327e..0cb199a 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2336,14 +2336,14 @@ in-memory footprint at the cost of packing and unpacking.") (define-public vg (package (name "vg") - (version "1.50.0") + (version "1.61.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "1n06fh6qvffhbxy7m096r8cy16wi0nm6gfgi3rsjy9zrb7g1jzhs")) + (base32 "1yb8ffqq65ma5di42qlj483x42viq5j4xyyg3vpww60gm15n1yxx")) (snippet #~(begin (use-modules (guix build utils)) @@ -2355,6 +2355,11 @@ in-memory footprint at the cost of packing and unpacking.") (build-system gnu-build-system) (arguments (list + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + ;; Set rpath so the validate-runpath phase finds + ;; libhandlegraph.so. + (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")) #:phases #~(modify-phases %standard-phases (delete 'configure) ; no configure script @@ -2429,7 +2434,16 @@ in-memory footprint at the cost of packing and unpacking.") ((" \\$\\(LIB_DIR\\)/libraptor2.a") (string-append " " (search-input-file inputs "/lib/libraptor2.so"))) ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (search-input-file inputs "/bin/rapper")))))) + (string-append " " (search-input-file inputs "/bin/rapper")))) + ;; Create obj and lib directories. They do not exist in + ;; the release tarball. + (mkdir "deps/libbdsg/bdsg/obj") + (mkdir "deps/libbdsg/lib") + ;; Do not remove obj and lib directories in the clean + ;; target. + (substitute* "deps/libbdsg/Makefile" + (("\\[ ! -e \\$\\(OBJ_DIR\\) \\][^\n]*") "") + (("\\[ ! -e \\$\\(LIB_DIR\\) \\][^\n]*") "")))) (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("deps/mmmultimap/CMakeLists.txt" @@ -2495,6 +2509,7 @@ 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/libhandlegraph.so" (string-append out "/lib")) (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) |