diff options
Diffstat (limited to '.guix')
| -rw-r--r-- | .guix/domagi-package.scm | 95 | ||||
| -rw-r--r-- | .guix/odgi-package.scm | 72 |
2 files changed, 167 insertions, 0 deletions
diff --git a/.guix/domagi-package.scm b/.guix/domagi-package.scm new file mode 100644 index 0000000..2bbed06 --- /dev/null +++ b/.guix/domagi-package.scm @@ -0,0 +1,95 @@ +;;; domagi --- DuckDB-powered pangenome Swiss Army knife +;;; Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of domagi. +;;; +;;; domagi is free software: you can redistribute it and/or modify it under the +;;; terms of the GNU General Public License as published by the Free Software +;;; Foundation, either version 3 of the License, or (at your option) any later +;;; version. +;;; +;;; domagi is distributed in the hope that it will be useful, but WITHOUT ANY +;;; WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +;;; FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +;;; details. +;;; +;;; You should have received a copy of the GNU General Public License along with +;;; domagi. If not, see <https://www.gnu.org/licenses/>. + +(define-module (domagi-package) + #:use-module ((gnu packages check) #:select (python-pytest)) + #:use-module ((gnu packages cmake) #:select (cmake)) + #:use-module ((gnu packages duckdb) #:select (duckdb python-duckdb)) + #:use-module ((gnu packages pkg-config) #:select (pkg-config)) + #:use-module ((gnu packages python-xyz) #:select (python-click python-meson)) + #:use-module (guix build-system copy) + #:use-module (guix build-system pyproject) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils)) + +(define-public verstable + (package + (name "verstable") + (version "2.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JacksonAllan/Verstable") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0lwh9kh0jl2vxcijd8606h5xvsjxxa051qaqlx82cl36nh0hkkxp")))) + (build-system copy-build-system) + (arguments + (list #:install-plan + #~'(("verstable.h" "include/verstable.h")))) + (home-page "https://github.com/JacksonAllan/Verstable") + (synopsis "Generic C hash table library") + (description "Verstable is a versatile generic hash table intended +to bring the speed and memory efficiency of state-of-the-art C++ hash +tables such as Abseil/Swiss, Boost, and Bytell to C. + +Its features include: +@begin itemize +@item Type safety +@item Customizable hash, comparison, and destructor functions +@item Single header +@item C99 compatibility +@item Generic API in C11 and later +@item High speed mostly impervious to load factor +@item Only two bytes of overhead per bucket +@item Tombstone-free deletion +@end itemize") + (license license:expat))) + +(define-public domagi + (package + (name "domagi") + (version "0.1.0") + (source (local-file ".." + "domagi-checkout" + #:recursive? #t + #:select? (or (git-predicate (dirname (current-source-directory))) + (const #t)))) + (build-system pyproject-build-system) + (inputs + (list duckdb + python-click + python-duckdb)) + (native-inputs + (list cmake + python-meson + pkg-config + python-pytest + verstable)) + (home-page "https://github.com/arunisaac/domagi") + (synopsis "DuckDB-powered pangenome Swiss Army knife") + (description "domagi is a DuckDB-powered clone of odgi, the pangenome +manipulation tool.") + (license license:gpl3+))) + +domagi 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 |