diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 362 |
2 files changed, 368 insertions, 6 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 01e4c59..e8df572 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -462,7 +462,7 @@ reads.") (define-public gfaffix (package (name "gfaffix") - (version "0.1.2.2") + (version "0.1.3") (source (origin (method git-fetch) @@ -471,7 +471,7 @@ reads.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1sh244yyhkaxbd635qjyig0wyxc57h8r1pwvs1vgdvlniw6h2cxy")) + (base32 "1biss5qv6ag1dfkn1nspwd528hpzgn8i4jydvbv2z7yv7sc685rh")) (modules '((guix build utils))) (snippet '(begin @@ -479,8 +479,9 @@ reads.") (("^handlegraph.*") "handlegraph = \"0.7\"\n")))))) (build-system cargo-build-system) (arguments - `(#:cargo-inputs - (("rust-clap" ,rust-clap-3) + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-3.1) ("rust-rustc-hash" ,rust-rustc-hash-1) ("rust-regex" ,rust-regex-1) ("rust-handlegraph" ,rust-handlegraph-0.7) @@ -495,8 +496,7 @@ reads.") (let ((handlebar-version ,(package-version rust-handlegraph-0.7))) (substitute* "Cargo.toml" (("\"0.7\"") - (string-append "{ version = \"" handlebar-version "\" }"))) - #t)))))) + (string-append "{ version = \"" handlebar-version "\" }"))))))))) (home-page "https://github.com/marschall-lab/GFAffix") (synopsis "Identify walk-preserving shared affixes in variation graphs") (description diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 2d14065..e8b7722 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -140,3 +140,365 @@ or any combination.") (description "Rust CLI tools for manipulation of Jupyter Notebooks.") (license #f)))) ; There is no license. +(define-public rust-clap-3.1 + (package + (name "rust-clap") + (version "3.1.6") + (source + (origin + (method url-fetch) + (uri (crate-uri "clap" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "08q1hkksfixybnrwrpm44xq028wbn9yr2hnzrax9hihyq8v39jfq")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Skip the tests for now + #:cargo-inputs + (("rust-atty" ,rust-atty-0.2) + ("rust-backtrace" ,rust-backtrace-0.3) + ("rust-bitflags" ,rust-bitflags-1) + ("rust-clap-derive" ,rust-clap-derive-3.1) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-os-str-bytes" ,rust-os-str-bytes-6) + ("rust-regex" ,rust-regex-1) + ("rust-strsim" ,rust-strsim-0.10) + ("rust-termcolor" ,rust-termcolor-1) + ("rust-terminal-size" ,rust-terminal-size-0.1) + ("rust-textwrap" ,rust-textwrap-0.15) + ("rust-unicase" ,rust-unicase-2) + ("rust-yaml-rust" ,rust-yaml-rust-0.4)) + ;#:cargo-development-inputs + ;(("rust-criterion" ,rust-criterion-0.3) + ; ("rust-lazy-static" ,rust-lazy-static-1) + ; ("rust-regex" ,rust-regex-1) + ; ("rust-rustversion" ,rust-rustversion-1) + ; ("rust-trybuild" ,rust-trybuild-1) + ; ("rust-trycmd" ,rust-trycmd-0.12)) + )) + (home-page "https://github.com/clap-rs/clap") + (synopsis + "A simple to use, efficient, and full-featured Command Line Argument Parser") + (description + "This package provides a simple to use, efficient, and full-featured Command Line + Argument Parser") + (license (list license:expat license:asl2.0)))) + +(define-public rust-clap-derive-3.1 + (package + (name "rust-clap-derive") + (version "3.1.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "clap-derive" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "05mz2y6k73wc1gvv9r4mllfqslzvlwkvx77lk7769ag1xlwd15fs")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-heck" ,rust-heck-0.4) + ("rust-proc-macro-error" ,rust-proc-macro-error-1) + ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-quote" ,rust-quote-1) + ("rust-syn" ,rust-syn-1)))) + (home-page "https://github.com/clap-rs/clap/tree/master/clap_derive") + (synopsis + "Parse command line argument by defining a struct, derive crate.") + (description + "Parse command line argument by defining a struct, derive crate.") + (license (list license:expat license:asl2.0)))) + +(define-public rust-os-str-bytes-6 + (package + (name "rust-os-str-bytes") + (version "6.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "os-str-bytes" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0r5z5xds2wzzqlqjaw96dpjsz5nqyzc1rflm4mh09aa32qyl88lf")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-memchr" ,rust-memchr-2) + ("rust-print-bytes" ,rust-print-bytes-0.5) + ("rust-uniquote" ,rust-uniquote-3)) + #:cargo-development-inputs + (("rust-getrandom" ,rust-getrandom-0.2)))) + (home-page "https://github.com/dylni/os_str_bytes") + (synopsis + "Utilities for converting between byte sequences and platform-native strings") + (description + "Utilities for converting between byte sequences and platform-native strings") + (license (list license:expat license:asl2.0)))) + +(define-public rust-textwrap-0.15 + (package + (name "rust-textwrap") + (version "0.15.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "textwrap" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1yw513k61lfiwgqrfvsjw1a5wpvm0azhpjr2kr0jhnq9c56is55i")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Skip tests for now + #:cargo-inputs + (("rust-hyphenation" ,rust-hyphenation-0.8) + ("rust-smawk" ,rust-smawk-0.3) + ("rust-terminal-size" ,rust-terminal-size-0.1) + ("rust-unicode-linebreak" ,rust-unicode-linebreak-0.1) + ("rust-unicode-width" ,rust-unicode-width-0.1)) + ;#:cargo-development-inputs + ;(("rust-criterion" ,rust-criterion-0.3) + ; ("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)) + )) + (home-page "https://github.com/mgeisler/textwrap") + (synopsis + "Powerful library for word wrapping, indenting, and dedenting strings") + (description + "Powerful library for word wrapping, indenting, and dedenting strings") + (license license:expat))) + +(define-public rust-trycmd-0.12 + (package + (name "rust-trycmd") + (version "0.12.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "trycmd" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1rwa5nzq8c5zg7lqmpkf7hyib415yxshd9amp911y8w1zss4s38p")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-backtrace" ,rust-backtrace-0.3) + ("rust-concolor" ,rust-concolor-0.0.8) + ("rust-content-inspector" ,rust-content-inspector-0.2) + ("rust-difflib" ,rust-difflib-0.4) + ("rust-dunce" ,rust-dunce-1) + ("rust-escargot" ,rust-escargot-0.5) + ("rust-glob" ,rust-glob-0.3) + ("rust-humantime" ,rust-humantime-2) + ("rust-humantime-serde" ,rust-humantime-serde-1) + ("rust-normalize-line-endings" ,rust-normalize-line-endings-0.3) + ("rust-os-pipe" ,rust-os-pipe-1) + ("rust-rayon" ,rust-rayon-1) + ("rust-schemars" ,rust-schemars-0.8) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-shlex" ,rust-shlex-1) + ("rust-tempfile" ,rust-tempfile-3) + ("rust-toml-edit" ,rust-toml-edit-0.12) + ("rust-wait-timeout" ,rust-wait-timeout-0.2) + ("rust-walkdir" ,rust-walkdir-2) + ("rust-yansi" ,rust-yansi-0.5)))) + (home-page "https://github.com/assert-rs/trycmd") + (synopsis "Snapshot testing for a herd of CLI tests") + (description "Snapshot testing for a herd of CLI tests") + (license (list license:expat license:asl2.0)))) + +(define-public rust-smawk-0.3 + (package + (name "rust-smawk") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "smawk" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0hv0q1mw1r1brk7v3g4a80j162p7g1dri4bdidykrakzfqjd4ypn")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-ndarray" ,rust-ndarray-0.14)) + #:cargo-development-inputs + (("rust-num-traits" ,rust-num-traits-0.2) + ("rust-rand" ,rust-rand-0.8) + ("rust-rand-chacha" ,rust-rand-chacha-0.3) + ("rust-version-sync" ,rust-version-sync-0.9)))) + (home-page "https://github.com/mgeisler/smawk") + (synopsis "Functions for finding row-minima in a totally monotone matrix.") + (description + "This package provides functions for finding row-minima in a totally monotone +matrix.") + (license license:expat))) + +(define-public rust-unicode-linebreak-0.1 + (package + (name "rust-unicode-linebreak") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (crate-uri "unicode-linebreak" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0grq6bsn967q4vpifld53s7a140nlmpq5vy8ghgr73f4n2mdqlis")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-regex" ,rust-regex-1)))) + (home-page "https://github.com/axelf4/unicode-linebreak") + (synopsis "Implementation of the Unicode Line Breaking Algorithm") + (description "Implementation of the Unicode Line Breaking Algorithm") + (license license:asl2.0))) + +(define-public rust-lipsum-0.8 + (package + (name "rust-lipsum") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "lipsum" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0sn5k0hgx099x2qdx0xlx8a5b74sfc55qnbyrhnh72baqxqp5vj2")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-rand" ,rust-rand-0.8) + ("rust-rand-chacha" ,rust-rand-chacha-0.3)) + #:cargo-development-inputs + (("rust-version-sync" ,rust-version-sync-0.9)))) + (home-page "https://github.com/mgeisler/lipsum/") + (synopsis + "Lipsum is a lorem ipsum text generation library. Use this if you need +some filler text for your application. + +The text is generated using a simple Markov chain, which you can also +instantiate to generate your own pieces of pseudo-random text. +") + (description + "Lipsum is a lorem ipsum text generation library. Use this if you need some +filler text for your application. + +The text is generated using a simple Markov chain, which you can also +instantiate to generate your own pieces of pseudo-random text.") + (license license:expat))) + +(define-public rust-print-bytes-0.5 + (package + (name "rust-print-bytes") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "print-bytes" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0d4i9y3jx1chi6w97a8rgdbwm9g3cppr53rw53zl6fcaq31qx0b6")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Skip tests for now + #:cargo-inputs + (("rust-winapi" ,rust-winapi-0.3)) + ;#:cargo-development-inputs + ;(("rust-os-str-bytes" ,rust-os-str-bytes-4)) + )) + (home-page "https://github.com/dylni/print_bytes") + (synopsis "Print bytes as losslessly as possible") + (description "Print bytes as losslessly as possible") + (license (list license:expat license:asl2.0)))) + +(define-public rust-uniquote-3 + (package + (name "rust-uniquote") + (version "3.1.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "uniquote" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1bkl0n41yvs415mqny4b434kr456ysnb3dhic1zrrzppwx95jvxa")))) + (build-system cargo-build-system) + (home-page "https://github.com/dylni/uniquote") + (synopsis "Quote strings for clear display in output") + (description "Quote strings for clear display in output") + (license (list license:expat license:asl2.0)))) + +(define-public rust-ndarray-0.14 + (package + (name "rust-ndarray") + (version "0.14.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "ndarray" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "011wqzmrd9gpfcfvy1xfbskqfiahn96pmi2d0r9x34d682amq3bc")))) + (build-system cargo-build-system) + (arguments + `(#:skip-build? #t + #:cargo-inputs + (("rust-approx" ,rust-approx-0.4) + ;("rust-blas-src" ,rust-blas-src-0.6) + ("rust-cblas-sys" ,rust-cblas-sys-0.1) + ("rust-matrixmultiply" ,rust-matrixmultiply-0.2) + ("rust-num-complex" ,rust-num-complex-0.3) + ("rust-num-integer" ,rust-num-integer-0.1) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-rawpointer" ,rust-rawpointer-0.2) + ("rust-rayon" ,rust-rayon-1) + ("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-approx" ,rust-approx-0.4) + ("rust-defmac" ,rust-defmac-0.2) + ("rust-itertools" ,rust-itertools-0.9) + ("rust-quickcheck" ,rust-quickcheck-0.9)))) + (home-page "https://github.com/rust-ndarray/ndarray") + (synopsis + "An n-dimensional array for general elements and for numerics. Lightweight array views and slicing; views support chunking and splitting.") + (description + "An n-dimensional array for general elements and for numerics. Lightweight array +views and slicing; views support chunking and splitting.") + (license (list license:expat license:asl2.0)))) + +(define-public rust-version-sync-0.9 + (package + (name "rust-version-sync") + (version "0.9.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "version-sync" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1w0v20p6k13yhfmgmcwhgy3371znyqcn83lhrf47swq7xhf81l4r")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.8) + ("rust-regex" ,rust-regex-1) + ("rust-semver" ,rust-semver-1) + ("rust-syn" ,rust-syn-1) + ("rust-toml" ,rust-toml-0.5) + ("rust-url" ,rust-url-2)) + #:cargo-development-inputs + (("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://github.com/mgeisler/version-sync") + (synopsis + "Crate for ensuring that version numbers in README files and other files are kept in sync with the crate version.") + (description + "Crate for ensuring that version numbers in README files and other files are kept +in sync with the crate version.") + (license license:expat))) + |