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| author | Arun Isaac | 2026-07-12 02:07:47 +0100 |
|---|---|---|
| committer | Arun Isaac | 2026-07-27 23:30:30 +0100 |
| commit | 74391420fa9890d33e8d89a15c816e6378c7aaef (patch) | |
| tree | 763c16edbd68b615d53c40c8ece197a3877358da /.guix/odgi-package.scm | |
| download | domagi-74391420fa9890d33e8d89a15c816e6378c7aaef.tar.gz domagi-74391420fa9890d33e8d89a15c816e6378c7aaef.tar.lz domagi-74391420fa9890d33e8d89a15c816e6378c7aaef.zip | |
Initial commit
Diffstat (limited to '.guix/odgi-package.scm')
| -rw-r--r-- | .guix/odgi-package.scm | 72 |
1 files changed, 72 insertions, 0 deletions
diff --git a/.guix/odgi-package.scm b/.guix/odgi-package.scm new file mode 100644 index 0000000..5fa94d1 --- /dev/null +++ b/.guix/odgi-package.scm @@ -0,0 +1,72 @@ +;; This odgi package definition is from https://git.genenetwork.org/guix-bioinformatics/tree/gn/packages/pangenome.scm?id=e586976ac493d2f7480784f098d58c9fed065b02#n524 + +(define-module (odgi-package) + #:use-module ((gnu packages datastructures) + #:select (libdivsufsort sdsl-lite)) + #:use-module ((gnu packages jemalloc) #:select (jemalloc)) + #:use-module ((gnu packages mpi) #:select (openmpi)) + #:use-module ((gnu packages pkg-config) #:select (pkg-config)) + #:use-module ((gnu packages python) #:select (python)) + #:use-module ((gnu packages python-xyz) #:select (pybind11)) + #:use-module (guix build-system cmake) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public odgi + (package + (name "odgi") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pangenome/odgi/releases" + "/download/v" version + "/odgi-v" version ".tar.gz")) + (sha256 + (base32 + "0brg0sz45v1wv4ld3p4jwiab10nyp2f691zfwpiva6g6f71q3cbk")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* "CMakeLists.txt" + (("-march=native") "") + (("-msse4\\.2") "")))))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f + #:parallel-build? #f ; parallel build uses too much memory + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-gnuinstalldirs-macros + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(odgi\\)" all) + (string-append all "\ninclude(GNUInstallDirs)")) + (("LIBRARY DESTINATION lib") + "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}") + (("ARCHIVE DESTINATION lib") + "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}")))) + (add-after 'unpack 'link-to-libodgi + (lambda _ + (substitute* "CMakeLists.txt" + (("^ \\$<TARGET_OBJECTS:odgi_objs>.*") "") + (("target_link_libraries\\(odgi " all) + (string-append all "libodgi_shared ")))))))) + (native-inputs (list pkg-config)) + (inputs + (list jemalloc + libdivsufsort + openmpi + pybind11 + python + sdsl-lite)) + (properties '((tunable? . #t))) + (home-page "https://github.com/vgteam/odgi") + (synopsis "Optimized Dynamic Genome/Graph Implementation") + (description "odgi provides an efficient and succinct dynamic DNA +sequence graph model, as well as algorithms for pangenome analysis.") + (license license:expat))) + +odgi |
