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authorEfraim Flashner2023-09-21 10:31:05 +0300
committerEfraim Flashner2023-09-21 10:31:05 +0300
commit88f74e4ae05a562c4a4373b9e3b86bac4ea132b2 (patch)
tree022a737e627af86f93b9c9bac5411b677ac30d6e /gn
parentfa03e6f84c0ff8e1c168568fd33316c170014251 (diff)
downloadguix-bioinformatics-88f74e4ae05a562c4a4373b9e3b86bac4ea132b2.tar.gz
odgi: Update to 0.8.3.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm28
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))