diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 53 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 176 |
2 files changed, 229 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b5ea52f..b2950ee 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -8,6 +8,7 @@ #: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 gnu) #:use-module (guix build-system meson) @@ -15,6 +16,7 @@ #: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 java) #:use-module (gn packages python) #:use-module (gn packages twint) @@ -28,6 +30,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cran) + #:use-module (gnu packages crates-io) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) @@ -56,6 +59,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) + #:use-module (gnu packages rust) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages statistics) @@ -447,6 +451,55 @@ reads.") (define-public edirect-gn (deprecated-package "edirect-gn" edirect)) +(define-public gfaffix + (package + (name "gfaffix") + (version "0.1.2") + (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 "0xpzi0zvaa4pajs4vbp3vkwj2ha8pi62ly7bd8cpf3fi6r32pgdz")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "Cargo.toml" + (("^handlegraph.*") "handlegraph = \"0.7\"\n")))))) + (build-system cargo-build-system) + (arguments + `(#:rust ,rust-1.49 ; or later + #:cargo-inputs + (("rust-clap" ,rust-clap-3) + ("rust-rustc-hash" ,rust-rustc-hash-1) + ("rust-regex" ,rust-regex-1) + ("rust-handlegraph" ,rust-handlegraph-0.7) + ("rust-gfa" ,rust-gfa-0.10) + ("rust-quick-csv", rust-quick-csv-0.1) + ("rust-log" ,rust-log-0.4) + ("rust-env-logger" ,rust-env-logger-0.7)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-dependency-version + (lambda* (#:key inputs #:allow-other-keys) + ;; TODO: Replace the hardcoded version with logic. + (substitute* "Cargo.toml" + (("\"0.7\"") + "{ version = \"0.7.0-alpha.7\" }")) + #t))))) + (inputs + ;; rust-handlegraph@0.7 doesn't get picked up as a rust input. + `(("rust-handlegraph-0.7" ,rust-handlegraph-0.7))) + (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))) + ;; TODO: Unbundle zlib, bamtools, tclap (define-public sniffles (package diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm new file mode 100644 index 0000000..9a619b9 --- /dev/null +++ b/gn/packages/crates-io.scm @@ -0,0 +1,176 @@ +(define-module (gn packages crates-io) + #: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 (gnu packages crates-io) + #:use-module (gnu packages rust)) + + +(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-gfa-0.10 + (package + (name "rust-gfa") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "gfa" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1hadm6vfjwyqw41bqci18wb4wv80rydmrag7a5c02pdp1gid14fw")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-bstr" ,rust-bstr-0.2) + ("rust-bytemuck" ,rust-bytemuck-1) + ("rust-fnv" ,rust-fnv-1) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-memmap" ,rust-memmap-0.7) + ("rust-nom" ,rust-nom-5) + ("rust-regex" ,rust-regex-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1)) + #:cargo-development-inputs + (("rust-criterion" ,rust-criterion-0.3)))) + (home-page "https://github.com/chfi/rs-gfa") + (synopsis "Library for working with graphs in the GFA format") + (description + "This package proides a Rust llibrary for working with graphs in the +@acronym(GFA, Graphical Fragment Assembly} format.") + (license license:expat))) + +(define-public rust-handlegraph-0.7 + ;; After this commit try the next actual release. + (let ((commit "a7ca8da640ae442ffd3ef4f5f9f358cd37c7deee") + (revision "1")) + (package + (inherit rust-handlegraph-0.3) + (name "rust-handlegraph") + (version (git-version "0.7.0-alpha.7" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chfi/rs-handlegraph") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "19cxgysxam79k6skanh4q4hafi4aglzcmg5hmm3vfnrzbz9q6js0")))) + (arguments + `(#:rust ,rust-1.47 ; or later + #:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-boomphf" ,rust-boomphf-0.5) + ("rust-bstr" ,rust-bstr-0.2) + ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5) + ("rust-fnv" ,rust-fnv-1) + ("rust-gfa" ,rust-gfa-0.10) + ("rust-log" ,rust-log-0.4) + ("rust-rayon" ,rust-rayon-1) + ("rust-succinct" ,rust-succinct-0.5)) + #:cargo-development-inputs + (("rust-quickcheck" ,rust-quickcheck-0.9) + ("rust-rand" ,rust-rand-0.7))))))) + +(define-public rust-quick-csv-0.1 + (package + (name "rust-quick-csv") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "quick-csv" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "131k8zzlplk2h62wz813jbvm0sk7v3mixwhhq34y9lmp3mqbgx7d")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rustc-serialize" ,rust-rustc-serialize-0.3)))) + (home-page "https://github.com/tafia/quick-csv") + (synopsis "Quick csv reader and decoder") + (description "This package provides a quick csv reader and decoder in Rust.") + (license license:expat))) + +(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 "Succinct data structures for Rust.1") + (license (list license:expat license:asl2.0)))) + +(define-public rust-wyhash-0.5 + (package + (name "rust-wyhash") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "wyhash" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "15f26hvx6nyp4d6iswha7rm3psidxa2k2iab1f1aqgsyq9iy3xms")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rand-core" ,rust-rand-core-0.6)))) + (home-page "https://github.com/eldruin/wyhash-rs") + (synopsis "Rust implementation of the WyHash algorithm") + (description + "This package provides a Rust implementation of the WyHash fast portable +non-cryptographic hashing algorithm and random number generator.") + (license (list license:expat license:asl2.0)))) |