diff options
| -rw-r--r-- | gn/packages/crates-io.scm | 115 | ||||
| -rw-r--r-- | gn/packages/pangenome.scm | 15 |
2 files changed, 110 insertions, 20 deletions
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index b90589f..2ffd798 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -9,9 +9,39 @@ #:use-module (gnu packages crates-io) #:use-module (gnu packages maths)) +(define-public rust-boomphf-0.5 + (package + (name "rust-boomphf") + (version "0.5.9") + (source + (origin + (method url-fetch) + (uri (crate-uri "boomphf" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0braniw72g9yq5006sfgc1g8d4317bb524c694jw6nggizrvg3sf")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8) + ("rust-log" ,rust-log-0.4) + ("rust-rayon" ,rust-rayon-1) + ("rust-serde" ,rust-serde-1) + ("rust-wyhash" ,rust-wyhash-0.5)) + #:cargo-development-inputs + (("rust-bencher" ,rust-bencher-0.1) + ("rust-quickcheck" ,rust-quickcheck-1)))) + (home-page "https://github.com/10XGenomics/rust-boomphf") + (synopsis "Scalable and Efficient Minimal Perfect Hash Functions") + (description "This package provides a Rust implementation of +@url{https://arxiv.org/abs/1702.03154, fast and scalable minimal perfect hashing +for massive key sets}. It generates an @acronym{MPHF, minimal perfect hash +functions} for a collection of hashable objects.") + (license license:expat))) + (define-public rust-handlegraph-0.7 (package - (inherit rust-handlegraph-0.3) (name "rust-handlegraph") (version "0.7.0-alpha.9") (source @@ -23,6 +53,7 @@ (sha256 (base32 "1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs")))) + (build-system cargo-build-system) (arguments `(#:cargo-inputs (("rust-anyhow" ,rust-anyhow-1) @@ -36,7 +67,79 @@ ("rust-succinct" ,rust-succinct-0.5)) #:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.9) - ("rust-rand" ,rust-rand-0.7)))))) + ("rust-rand" ,rust-rand-0.7)))) + (home-page "https://github.com/chfi/rs-handlegraph") + (synopsis "Library for use in variation graphs") + (description + "This package provides a Rust implementation of VG handle graph.") + (license license:expat))) + +(define-public rust-handlegraph-0.3 + (package + (inherit rust-handlegraph-0.7) + (name "rust-handlegraph") + (version "0.3.0") + (source (origin + (method url-fetch) + (uri (crate-uri "handlegraph" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1sj100w4lpj7798pws85qrfrzsily5hhzh6j118rwf56sgic1yml")))) + (arguments + `(#:cargo-inputs + (("rust-bstr" ,rust-bstr-0.2) + ("rust-gfa" ,rust-gfa-0.6)))))) + +(define-public rust-kstring-1 + (package + (name "rust-kstring") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "kstring" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1r4n9fa5scikqvl736nxghcfa6s3b07xz61w43hyzs2qb3wmd3nk")))) + (build-system cargo-build-system) + (arguments + `(;#:skip-build? #t ; Uses unstable features. + #:cargo-inputs + (("rust-document-features" ,rust-document-features-0.2) + ("rust-serde" ,rust-serde-1) + ("rust-static-assertions" ,rust-static-assertions-1)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3) + ("rust-proptest" ,rust-proptest-1)))) + (home-page "https://github.com/cobalt-org/kstring") + (synopsis "String optimized for map keys") + (description "Key String provides a Rust package optimized for map keys.") + (license (list license:expat license:asl2.0)))) + +(define-public rust-succinct-0.5 + (package + (name "rust-succinct") + (version "0.5.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "succinct" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0654c9gq50x7djyf25zbzz3d2pc4x3z21wmjj3qbr6d9h4hbd63p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-byteorder" ,rust-byteorder-1) + ("rust-num-traits" ,rust-num-traits-0.2)) + #:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.9)))) + (home-page "https://github.com/tov/succinct-rs") + (synopsis "Succinct data structures for Rust") + (description "This package provides succinct data structures for Rust.") + (license (list license:expat license:asl2.0)))) (define-public rust-clap-for-jrep (package @@ -236,7 +339,7 @@ or any combination.") ("rust-unicode-width" ,rust-unicode-width-0.1)) #:cargo-development-inputs (("rust-criterion" ,rust-criterion-0.3) - ("rust-lipsum" ,rust-lipsum-0.8) + ;("rust-lipsum" ,rust-lipsum-0.8) ("rust-termion" ,rust-termion-1) ;("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9) ("rust-version-sync" ,rust-version-sync-0.9)))) @@ -260,9 +363,7 @@ or any combination.") (base32 "1rwa5nzq8c5zg7lqmpkf7hyib415yxshd9amp911y8w1zss4s38p")))) (build-system cargo-build-system) (arguments - `(;#:skip-build? #t ; Not all inputs at correct versions? - ;#:tests? #f ; Skip tests for now - #:cargo-inputs + `(#:cargo-inputs (("rust-backtrace" ,rust-backtrace-0.3) ("rust-concolor" ,rust-concolor-0.0.8) ("rust-content-inspector" ,rust-content-inspector-0.2) @@ -302,7 +403,7 @@ or any combination.") (base32 "0wx4wd849bmkqj0gdi041gmpfpvlyhy2ha4zpin69yw9d9npl8cl")))) (build-system cargo-build-system) (arguments - `(;#:skip-build? #t ; Not all inputs packaged + `(#:skip-build? #t ; Not all inputs packaged ;#:tests? #f ; Skip tests for now #:cargo-inputs (("rust-combine" ,rust-combine-4) diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index 69e3d81..c66b594 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -1,23 +1,12 @@ -;; Bioinformatics module +;; Pangenome module (define-module (gn packages pangenome) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) - #:use-module (guix utils) #:use-module (guix download) - #:use-module (guix git-download) #:use-module (guix build-system cargo) - #:use-module (guix build-system gnu) - #:use-module (guix graph) - #:use-module (guix scripts graph) - #:use-module (guix store) - #:use-module (guix gexp) - #:use-module (gnu packages) - #:use-module (gnu packages base) #:use-module (gnu packages crates-io) - #:use-module (gnu packages rust) - #:use-module (gnu packages version-control) - #:use-module (srfi srfi-1)) + #:use-module (gn packages crates-io)) (define-public gfautil |