diff options
| author | Efraim Flashner | 2023-09-21 10:31:05 +0300 |
|---|---|---|
| committer | Efraim Flashner | 2023-09-21 10:31:05 +0300 |
| commit | 88f74e4ae05a562c4a4373b9e3b86bac4ea132b2 (patch) | |
| tree | 022a737e627af86f93b9c9bac5411b677ac30d6e /gn/packages | |
| parent | fa03e6f84c0ff8e1c168568fd33316c170014251 (diff) | |
| download | guix-bioinformatics-88f74e4ae05a562c4a4373b9e3b86bac4ea132b2.tar.gz | |
odgi: Update to 0.8.3.
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 28 |
1 files changed, 22 insertions, 6 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 8a4b278..dba5f6f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2033,32 +2033,48 @@ available to other researchers.") (delete-file "scanpy/tests/test_pca.py") #t))))))))) -;; TODO: Unbundle everything +;; TODO: Unbundle everything before upstreaming (define-public odgi (package (name "odgi") - (version "0.8.1") + (version "0.8.3") + (outputs '("out" "static")) (source (origin (method url-fetch) (uri (string-append "https://github.com/pangenome/odgi/releases" "/download/v" version "/odgi-v" version ".tar.gz")) (sha256 - (base32 "175083pb9hp0vn9a00hbxlayyk5a5j8p52yq5qfmbnfvndisbmbv")) + (base32 "1gw1xdb945z25rar6pba6kq5xdx8l7fkhxjyrvc1z1brva53p9hk")) (snippet #~(begin (use-modules (guix build utils)) (substitute* "CMakeLists.txt" (("-march=native") "") - (("-msse4\\.2") "")) - (delete-file-recursively "deps/pybind11") - (delete-file-recursively "deps/sdsl-lite"))))) + (("-msse4\\.2") "")))))) (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'link-to-libodgi + (lambda _ + ;; This lets us provide libraries for different psABI levels. + (substitute* "CMakeLists.txt" + (("^ \\$<TARGET_OBJECTS:odgi_objs>.*") "") + (("target_link_libraries\\(odgi " all) + (string-append all "libodgi_shared "))))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append #$output:static "/lib")) + (rename-file (string-append #$output "/lib/libodgi.a") + (string-append #$output:static "/lib/libodgi.a"))))))) (native-inputs (list pkg-config)) (inputs (list jemalloc libdivsufsort + openmpi pybind11 python sdsl-lite)) |