From 4f9f2d7ecdebc2be6a35eb5ad67dcd253bfa6d83 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 2 Apr 2026 11:42:26 +0200 Subject: Move (gfaffix) to rust package --- gn/packages/bioinformatics.scm | 25 ----- gn/packages/pangenome-rust.scm | 214 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 214 insertions(+), 25 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a50a44d..83dd2b8 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -635,31 +635,6 @@ integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.") (license license:gpl3+)))) -(define-public gfaffix - (package - (name "gfaffix") - (version "0.2.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/marschall-lab/GFAffix") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0yn8i70ww3x544qm4fwr33vklsxf3fvivpfpv46prkfz9hsmd9ps")))) - (build-system cargo-build-system) - (arguments - `(#:install-source? #f)) - (inputs (cargo-inputs 'gfaffix - #:module '(gn packages rust-crates))) - (home-page "https://github.com/marschall-lab/GFAffix") - (synopsis "Identify walk-preserving shared affixes in variation graphs") - (description - "GFAffix identifies walk-preserving shared affixes in variation graphs and -collapses them into a non-redundant graph structure.") - (license license:expat))) - (define-public graphaligner (package (name "graphaligner") diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index 41092bf..1399f24 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -2096,6 +2096,93 @@ (crate-source "unicode-width" "0.1.14" "1bzn2zv0gp8xxbxbhifw778a7fc93pa6a1kj24jgg9msj07f7mkx")) +;;; Crate sources for gfaffix + +(define rust-anyhow-1.0.101 + (crate-source "anyhow" "1.0.101" + "1skmg90fnjnlgs3vl7bksw7036d3rqwqj20n2fxd2ppg67p0y3jz")) + +(define rust-clap-4.5.59 + (crate-source "clap" "4.5.59" + "16b4kgj909yyshz9kj7nkalbyi46yz1lrhqha54wbbn32x6zgjn5")) + +(define rust-clap-builder-4.5.59 + (crate-source "clap_builder" "4.5.59" + "094fc76nsq3v52r1a9rbwix22cqnda8p2wr2a24j302v0r2sl39p")) + +(define rust-jiff-0.2.20 + (crate-source "jiff" "0.2.20" + "0hv59kcqj5sc0jgk4q7yrq5dp8yb3qlan98qk3s36sq9ribc6ry8")) + +(define rust-jiff-static-0.2.20 + (crate-source "jiff-static" "0.2.20" + "1rcvbp9aj8ll4ljxcgzq4l2h9idmkb0v6mdvf3r3i5r64m1np57p")) + +(define rust-regex-syntax-0.8.9 + (crate-source "regex-syntax" "0.8.9" + "0k0a47r1rcl794wj8a948niakbg081s5pp5nlgcbmmr2iy3qfs59")) + +(define rust-rustix-1.1.3 + (crate-source "rustix" "1.1.3" + "0d0z2zcw4rwzni1hm8snw8xdxwwrij336m31c4ghq66cghj9wv0l")) + +(define rust-syn-2.0.116 + (crate-source "syn" "2.0.116" + "1jv9pk48qmhn6yrdfl3lngy5i74wg7gcx13gfhvm4s8q0p3j9x1x")) + +(define rust-terminal-size-0.4.3 + (crate-source "terminal_size" "0.4.3" + "1l7cicmz49c0cyskfp5a389rsai649xi7y032v73475ikjbwpf30")) + +(define rust-windows-aarch64-gnullvm-0.53.1 + (crate-source "windows_aarch64_gnullvm" "0.53.1" + "0lqvdm510mka9w26vmga7hbkmrw9glzc90l4gya5qbxlm1pl3n59" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-aarch64-msvc-0.53.1 + (crate-source "windows_aarch64_msvc" "0.53.1" + "01jh2adlwx043rji888b22whx4bm8alrk3khjpik5xn20kl85mxr" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-i686-gnu-0.53.1 + (crate-source "windows_i686_gnu" "0.53.1" + "18wkcm82ldyg4figcsidzwbg1pqd49jpm98crfz0j7nqd6h6s3ln" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-i686-gnullvm-0.53.1 + (crate-source "windows_i686_gnullvm" "0.53.1" + "030qaxqc4salz6l4immfb6sykc6gmhyir9wzn2w8mxj8038mjwzs" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-i686-msvc-0.53.1 + (crate-source "windows_i686_msvc" "0.53.1" + "1hi6scw3mn2pbdl30ji5i4y8vvspb9b66l98kkz350pig58wfyhy" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-targets-0.53.5 + (crate-source "windows-targets" "0.53.5" + "1wv9j2gv3l6wj3gkw5j1kr6ymb5q6dfc42yvydjhv3mqa7szjia9")) + +(define rust-windows-x86-64-gnu-0.53.1 + (crate-source "windows_x86_64_gnu" "0.53.1" + "16d4yiysmfdlsrghndr97y57gh3kljkwhfdbcs05m1jasz6l4f4w" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-x86-64-gnullvm-0.53.1 + (crate-source "windows_x86_64_gnullvm" "0.53.1" + "1qbspgv4g3q0vygkg8rnql5c6z3caqv38japiynyivh75ng1gyhg" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-windows-x86-64-msvc-0.53.1 + (crate-source "windows_x86_64_msvc" "0.53.1" + "0l6npq76vlq4ksn4bwsncpr8508mk0gmznm6wnhjg95d19gzzfyn" + #:snippet '(delete-file-recursively "lib"))) + +(define rust-libz-sys-1.1.23 + ;; TODO: Check bundled sources. + (crate-source "libz-sys" "1.1.23" + "1xy0l46gmhfyk28r9pm7njl0h7dh8l2vpiqw67kn043pyfxiil8m")) + (define-cargo-inputs lookup-cargo-inputs (gfainject => (list rust-adler-1.0.2 @@ -2768,6 +2855,108 @@ rust-wit-bindgen-rust-macro-0.51.0 rust-wit-component-0.244.0 rust-wit-parser-0.244.0)) + (gfaffix => + (list rust-adler2-2.0.1 + rust-aho-corasick-1.1.4 + rust-anstream-0.6.21 + rust-anstyle-1.0.13 + rust-anstyle-parse-0.2.7 + rust-anstyle-query-1.1.5 + rust-anstyle-wincon-3.0.11 + rust-anyhow-1.0.101 + rust-arrayvec-0.5.2 + rust-autocfg-1.5.0 + rust-bitflags-1.3.2 + rust-bitflags-2.11.0 + rust-boomphf-0.5.9 + rust-bstr-0.2.17 + rust-bytemuck-1.25.0 + rust-bytemuck-derive-1.10.2 + rust-byteorder-1.5.0 + rust-cc-1.2.56 + rust-cfg-if-1.0.4 + rust-clap-4.5.59 + rust-clap-builder-4.5.59 + rust-clap-derive-4.5.55 + rust-clap-lex-1.0.0 + rust-colorchoice-1.0.4 + rust-crc32fast-1.5.0 + rust-crossbeam-channel-0.5.15 + rust-crossbeam-deque-0.8.6 + rust-crossbeam-epoch-0.9.18 + rust-crossbeam-utils-0.8.21 + rust-either-1.15.0 + rust-env-filter-1.0.0 + rust-env-logger-0.11.9 + rust-equivalent-1.0.2 + rust-errno-0.3.14 + rust-find-msvc-tools-0.1.9 + rust-flate2-1.1.9 + rust-fnv-1.0.7 + rust-gfa-0.10.1 + rust-handlegraph-0.7.0-alpha.9 + rust-hashbrown-0.16.1 + rust-heck-0.5.0 + rust-indexmap-2.13.0 + rust-is-terminal-polyfill-1.70.2 + rust-jiff-0.2.20 + rust-jiff-static-0.2.20 + rust-lazy-static-1.5.0 + rust-lexical-core-0.7.6 + rust-libc-0.2.182 + rust-libz-sys-1.1.23 + rust-linux-raw-sys-0.11.0 + rust-log-0.4.29 + rust-memchr-2.8.0 + rust-memmap-0.7.0 + rust-miniz-oxide-0.8.9 + rust-nom-5.1.3 + rust-num-traits-0.2.19 + rust-once-cell-polyfill-1.70.2 + rust-pkg-config-0.3.32 + rust-portable-atomic-1.13.1 + rust-portable-atomic-util-0.2.5 + rust-proc-macro2-1.0.106 + rust-quote-1.0.44 + rust-rand-core-0.6.4 + rust-rayon-1.11.0 + rust-rayon-core-1.13.0 + rust-regex-1.12.3 + rust-regex-automata-0.1.10 + rust-regex-automata-0.4.14 + rust-regex-syntax-0.8.9 + rust-rustc-hash-2.1.1 + rust-rustix-1.1.3 + rust-ryu-1.0.23 + rust-serde-core-1.0.228 + rust-serde-derive-1.0.228 + rust-shlex-1.3.0 + rust-simd-adler32-0.3.8 + rust-static-assertions-1.1.0 + rust-strsim-0.11.1 + rust-succinct-0.5.2 + rust-syn-2.0.116 + rust-terminal-size-0.4.3 + rust-unicode-ident-1.0.24 + rust-utf8parse-0.2.2 + rust-vcpkg-0.2.15 + rust-version-check-0.9.5 + rust-winapi-0.3.9 + rust-winapi-i686-pc-windows-gnu-0.4.0 + rust-winapi-x86-64-pc-windows-gnu-0.4.0 + rust-windows-link-0.2.1 + rust-windows-sys-0.60.2 + rust-windows-sys-0.61.2 + rust-windows-targets-0.53.5 + rust-windows-aarch64-gnullvm-0.53.1 + rust-windows-aarch64-msvc-0.53.1 + rust-windows-i686-gnu-0.53.1 + rust-windows-i686-gnullvm-0.53.1 + rust-windows-i686-msvc-0.53.1 + rust-windows-x86-64-gnu-0.53.1 + rust-windows-x86-64-gnullvm-0.53.1 + rust-windows-x86-64-msvc-0.53.1 + rust-wyhash-0.5.0)) (gfautil => (list rust-aho-corasick-1.1.4 rust-android-system-properties-0.1.5 @@ -3373,3 +3562,28 @@ and alignments for analysis. It can also compute graphs for the sequences.") "This package provides command line tools for working with @acronym{GFA, Graphical Fragment Assembly} files and related formats.") (license license:expat)))) + +(define-public gfaffix + (package + (name "gfaffix") + (version "0.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marschall-lab/GFAffix") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0yn8i70ww3x544qm4fwr33vklsxf3fvivpfpv46prkfz9hsmd9ps")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f)) + (inputs (cargo-inputs 'gfaffix + #:module '(gn packages pangenome-rust))) + (home-page "https://github.com/marschall-lab/GFAffix") + (synopsis "Identify walk-preserving shared affixes in variation graphs") + (description + "GFAffix identifies walk-preserving shared affixes in variation graphs and +collapses them into a non-redundant graph structure.") + (license license:expat))) -- cgit 1.4.1