diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 3 | ||||
| -rw-r--r-- | gn/packages/genenetwork-rust.scm | 260 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 5 |
3 files changed, 261 insertions, 7 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 83dd2b8..8b1a2db 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -9,7 +9,6 @@ #:use-module (guix git-download) #:use-module (guix hg-download) #:use-module (guix build-system ant) - #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) #:use-module (guix build-system copy) #:use-module (guix build-system gnu) @@ -21,7 +20,6 @@ #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) - #:use-module (gn packages crates-io) #:use-module (gn packages datastructures) #:use-module (gn packages maths) #:use-module (gn packages python) @@ -40,7 +38,6 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpp) #:use-module (gnu packages cran) - #:use-module (past-crates packages crates-io) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) diff --git a/gn/packages/genenetwork-rust.scm b/gn/packages/genenetwork-rust.scm index 6189c72..54b8389 100644 --- a/gn/packages/genenetwork-rust.scm +++ b/gn/packages/genenetwork-rust.scm @@ -8,6 +8,7 @@ #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix gexp) + #:use-module (gnu packages maths) #:export (lookup-cargo-inputs)) ;;; Crate sources for rust-qtlreaper (guix import crate -f Cargo.lock qtlreaper) @@ -249,6 +250,169 @@ "1amb5i6gz7yjb0dnmz5y669674pqmwbj44p4yfxfv2ncgvk8x15q")) + +;;; Crate sources for gn-rust-correlation + +(define rust-gsl-6.0.0 + (crate-source "GSL" "6.0.0" + "1kpiivagrsk9ags7d4k2521jwix0lqgnd3i8ayj3dfniszvcmgn9")) + +(define rust-gsl-sys-3.0.0 + ;; TODO REVIEW: Check bundled sources. + (crate-source "GSL-sys" "3.0.0" + "17dx066l1pbjwp9syjkzqb6fiajyb4wc814zqdfrj807rh6nfxs5")) + +(define rust-aho-corasick-1.1.4 + (crate-source "aho-corasick" "1.1.4" + "00a32wb2h07im3skkikc495jvncf62jl6s96vwc7bhi70h9imlyx")) + +(define rust-assert-approx-eq-1.1.0 + (crate-source "assert_approx_eq" "1.1.0" + "1zagfwfad5wssmr830gk3489f97ppczv6xs627jxniwm6ssdl1rw")) + +(define rust-bumpalo-3.20.2 + (crate-source "bumpalo" "3.20.2" + "1jrgxlff76k9glam0akhwpil2fr1w32gbjdf5hpipc7ld2c7h82x")) + +(define rust-cast-0.3.0 + (crate-source "cast" "0.3.0" + "1dbyngbyz2qkk0jn2sxil8vrz3rnpcj142y184p9l4nbl9radcip")) + +(define rust-cfg-if-1.0.4 + (crate-source "cfg-if" "1.0.4" + "008q28ajc546z5p2hcwdnckmg0hia7rnx52fni04bwqkzyrghc4k")) + +(define rust-criterion-0.3.6 + (crate-source "criterion" "0.3.6" + "13yd64ah93gkbdv7qq4cr6rhgl9979jjcjk3gkhnav1b7glns7dh")) + +(define rust-criterion-plot-0.4.5 + (crate-source "criterion-plot" "0.4.5" + "0xhq0jz1603585h7xvm3s4x9irmifjliklszbzs4cda00y1cqwr6")) + +(define rust-csv-1.4.0 + (crate-source "csv" "1.4.0" + "0f7r2ip0rbi7k377c3xmsh9xd69sillffhpfmbgnvz3yrxl9vkaj")) + +(define rust-csv-core-0.1.13 + (crate-source "csv-core" "0.1.13" + "10lppd3fdb1i5npgx9xqjs5mjmy2qbdi8n16i48lg03ak4k3qjkh")) + +(define rust-half-1.8.3 + (crate-source "half" "1.8.3" + "00q4ki8ycdswapw6xn1q89vr7rzi1c8m99igps0lx1i1gzhyshqv")) + +(define rust-itertools-0.10.5 + (crate-source "itertools" "0.10.5" + "0ww45h7nxx5kj6z2y6chlskxd1igvs4j507anr6dzg99x1h25zdh")) + +(define rust-js-sys-0.3.94 + ;; TODO REVIEW: Check bundled sources. + (crate-source "js-sys" "0.3.94" + "1nb4fr7c78mrrdhmg04nbac1zvd5z3panvqka8sy30nfh3py411f")) + +(define rust-lazy-static-1.5.0 + (crate-source "lazy_static" "1.5.0" + "1zk6dqqni0193xg6iijh7i3i44sryglwgvx20spdvwk3r6sbrlmv")) + +(define rust-once-cell-1.21.4 + (crate-source "once_cell" "1.21.4" + "0l1v676wf71kjg2khch4dphwh1jp3291ffiymr2mvy1kxd5kwz4z")) + +(define rust-oorandom-11.1.5 + (crate-source "oorandom" "11.1.5" + "07mlf13z453fq01qff38big1lh83j8l6aaglf63ksqzzqxc0yyfn")) + +(define rust-paste-1.0.15 + (crate-source "paste" "1.0.15" + "02pxffpdqkapy292harq6asfjvadgp1s005fip9ljfsn9fvxgh2p")) + +(define rust-pkg-config-0.3.32 + (crate-source "pkg-config" "0.3.32" + "0k4h3gnzs94sjb2ix6jyksacs52cf1fanpwsmlhjnwrdnp8dppby")) + +(define rust-plotters-0.3.7 + (crate-source "plotters" "0.3.7" + "0ixpy9svpmr2rkzkxvvdpysjjky4gw104d73n7pi2jbs7m06zsss")) + +(define rust-plotters-backend-0.3.7 + (crate-source "plotters-backend" "0.3.7" + "0ahpliim4hrrf7d4ispc2hwr7rzkn6d6nf7lyyrid2lm28yf2hnz")) + +(define rust-plotters-svg-0.3.7 + (crate-source "plotters-svg" "0.3.7" + "0w56sxaa2crpasa1zj0bhxzihlapqfkncggavyngg0w86anf5fji")) + +(define rust-regex-1.12.3 + (crate-source "regex" "1.12.3" + "0xp2q0x7ybmpa5zlgaz00p8zswcirj9h8nry3rxxsdwi9fhm81z1")) + +(define rust-regex-automata-0.4.14 + (crate-source "regex-automata" "0.4.14" + "13xf7hhn4qmgfh784llcp2kzrvljd13lb2b1ca0mwnf15w9d87bf")) + +(define rust-regex-syntax-0.8.10 + (crate-source "regex-syntax" "0.8.10" + "02jx311ka0daxxc7v45ikzhcl3iydjbbb0mdrpc1xgg8v7c7v2fw")) + +(define rust-rustversion-1.0.22 + (crate-source "rustversion" "1.0.22" + "0vfl70jhv72scd9rfqgr2n11m5i9l1acnk684m2w83w0zbqdx75k")) + +(define rust-ryu-1.0.23 + (crate-source "ryu" "1.0.23" + "0zs70sg00l2fb9jwrf6cbkdyscjs53anrvai2hf7npyyfi5blx4p")) + +(define rust-same-file-1.0.6 + (crate-source "same-file" "1.0.6" + "00h5j1w87dmhnvbv9l8bic3y7xxsnjmssvifw2ayvgx9mb1ivz4k")) + +(define rust-serde-cbor-0.11.2 + (crate-source "serde_cbor" "0.11.2" + "1xf1bq7ixha30914pd5jl3yw9v1x6car7xgrpimvfvs5vszjxvrb")) + +(define rust-tinytemplate-1.2.1 + (crate-source "tinytemplate" "1.2.1" + "1g5n77cqkdh9hy75zdb01adxn45mkh9y40wdr7l68xpz35gnnkdy")) + +(define rust-walkdir-2.5.0 + (crate-source "walkdir" "2.5.0" + "0jsy7a710qv8gld5957ybrnc07gavppp963gs32xk4ag8130jy99")) + +(define rust-wasm-bindgen-0.2.117 + (crate-source "wasm-bindgen" "0.2.117" + "1c6hi55mq70546hrvrx7wa27sn3yvf04gg6hf8riwn8mnhdzql85")) + +(define rust-wasm-bindgen-macro-0.2.117 + (crate-source "wasm-bindgen-macro" "0.2.117" + "1gl6gqy60khhyqv354m0kmgk541sass8kzymxim7hi6zbaizkgbz")) + +(define rust-wasm-bindgen-macro-support-0.2.117 + (crate-source "wasm-bindgen-macro-support" "0.2.117" + "1wlza8xdr18cac2wm3ahxdwx1nnqa01m0d3jf3kd9dmsy8z6kafw")) + +(define rust-wasm-bindgen-shared-0.2.117 + (crate-source "wasm-bindgen-shared" "0.2.117" + "0frxrdi1w0cswv8v7n1972hd23nbwm8hr7a2dhdq8bbd59l9l4ir")) + +(define rust-web-sys-0.3.94 + ;; TODO REVIEW: Check bundled sources. + (crate-source "web-sys" "0.3.94" + "02nxnhv349r2gcy8w71cjj6nimww1g2zy20y8r4hhbxi75z04w6d")) + +(define rust-winapi-util-0.1.11 + (crate-source "winapi-util" "0.1.11" + "08hdl7mkll7pz8whg869h58c1r9y7in0w0pk8fm24qc77k0b39y2")) + +(define rust-windows-link-0.2.1 + (crate-source "windows-link" "0.2.1" + "1rag186yfr3xx7piv5rg8b6im2dwcf8zldiflvb22xbzwli5507h")) + +(define rust-windows-sys-0.61.2 + ;; TODO REVIEW: Check bundled sources. + (crate-source "windows-sys" "0.61.2" + "1z7k3y9b6b5h52kid57lvmvm05362zv1v8w0gc7xyv5xphlp44xf")) + (define-cargo-inputs lookup-cargo-inputs (qtlreaper => (list rust-ansi-term-0.12.1 @@ -311,6 +475,83 @@ rust-winapi-x86-64-pc-windows-gnu-0.4.0 rust-zmij-1.0.21 )) + (correlation_rust => + (list rust-aho-corasick-1.1.4 + rust-assert-approx-eq-1.1.0 + rust-atty-0.2.14 + rust-autocfg-1.5.0 + rust-bitflags-1.3.2 + rust-bumpalo-3.20.2 + rust-cast-0.3.0 + rust-cfg-if-1.0.4 + rust-clap-2.34.0 + rust-crossbeam-deque-0.8.6 + rust-crossbeam-epoch-0.9.18 + rust-crossbeam-utils-0.8.21 + rust-criterion-0.3.6 + rust-criterion-plot-0.4.5 + rust-csv-1.4.0 + rust-csv-core-0.1.13 + rust-either-1.15.0 + rust-gsl-6.0.0 + rust-gsl-sys-3.0.0 + rust-half-1.8.3 + rust-heck-0.3.3 + rust-hermit-abi-0.1.19 + rust-itertools-0.10.5 + rust-itoa-1.0.18 + rust-js-sys-0.3.94 + rust-lazy-static-1.5.0 + rust-libc-0.2.184 + rust-memchr-2.8.0 + rust-num-traits-0.2.19 + rust-once-cell-1.21.4 + rust-oorandom-11.1.5 + rust-paste-1.0.15 + rust-pkg-config-0.3.32 + rust-plotters-0.3.7 + rust-plotters-backend-0.3.7 + rust-plotters-svg-0.3.7 + rust-proc-macro2-1.0.106 + rust-quote-1.0.45 + rust-rayon-1.11.0 + rust-rayon-core-1.13.0 + rust-regex-1.12.3 + rust-regex-automata-0.4.14 + rust-regex-syntax-0.8.10 + rust-rustversion-1.0.22 + rust-ryu-1.0.23 + rust-same-file-1.0.6 + rust-serde-1.0.228 + rust-serde-cbor-0.11.2 + rust-serde-core-1.0.228 + rust-serde-derive-1.0.228 + rust-serde-json-1.0.149 + rust-strsim-0.8.0 + rust-structopt-0.2.18 + rust-structopt-derive-0.2.18 + rust-syn-0.15.44 + rust-syn-2.0.117 + rust-textwrap-0.11.0 + rust-tinytemplate-1.2.1 + rust-unicode-ident-1.0.24 + rust-unicode-segmentation-1.13.2 + rust-unicode-width-0.1.14 + rust-unicode-xid-0.1.0 + rust-vec-map-0.8.2 + rust-walkdir-2.5.0 + rust-wasm-bindgen-0.2.117 + rust-wasm-bindgen-macro-0.2.117 + rust-wasm-bindgen-macro-support-0.2.117 + rust-wasm-bindgen-shared-0.2.117 + rust-web-sys-0.3.94 + rust-winapi-0.3.9 + rust-winapi-i686-pc-windows-gnu-0.4.0 + rust-winapi-util-0.1.11 + rust-winapi-x86-64-pc-windows-gnu-0.4.0 + rust-windows-link-0.2.1 + rust-windows-sys-0.61.2 + rust-zmij-1.0.21)) ) (define-public rust-qtlreaper @@ -332,3 +573,22 @@ "Rust-qtlreaper is a Rust implementation of QTL Reaper for mapping quantitative trait loci (QTL) in genetic datasets.") (license license:agpl3+))) + +(define-public gn-rust-correlation + (let ((commit "48604d86471df965f189e46580578b24191add0e") + (revision "0")) + (package + (name "gn-rust-correlation") + (version (git-version "0.1.4" revision commit)) + ;; Use local source with updated Cargo.lock for modern Rust. + (source (local-file "/fast/pjotr/tmp/claude/factory/correlation_rust" + #:recursive? #t)) + (build-system cargo-build-system) + (native-inputs (list gsl)) + (arguments (list #:install-source? #f)) + (inputs (cargo-inputs 'correlation_rust + #:module '(gn packages genenetwork-rust))) + (home-page "https://github.com/Alexanderlacuna/correlation_rust") + (synopsis "Re-implementation of genenetwork/correlation in Rust") + (description "Re-implementation of genenetwork/correlation in Rust.") + (license #f)))) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c1b3f83..d8c83ac 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -7,7 +7,6 @@ #:use-module (guix download) #:use-module (guix git) #:use-module (guix git-download) - #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (guix build-system trivial) @@ -24,7 +23,6 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages check) #:use-module (gnu packages cran) - #:use-module (past-crates packages crates-io) #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages ghostscript) @@ -52,7 +50,6 @@ #:use-module (gnu packages xml) #:use-module (gnu packages serialization) #:use-module (gn packages bioinformatics) - #:use-module (gn packages crates-io) #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages node) @@ -106,7 +103,7 @@ python-mysqlclient-2.2.7 python-numpy python-pandas - python-pingouin-without-tests + python-pingouin python-plotly python-pyld python-pymonad |