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authorEfraim Flashner2022-03-31 09:24:11 +0300
committerEfraim Flashner2022-03-31 09:24:11 +0300
commit5946e2eaa8d4db0b94fde58ddf118b8c5e552adf (patch)
treee89acd26a41ce971e01b64342f6ec3a5053474d1
parent7cbb463281d2aff8184f8c7689d1cfcb622de51c (diff)
downloadguix-bioinformatics-5946e2eaa8d4db0b94fde58ddf118b8c5e552adf.tar.gz
gn: Update gfaffix to 0.1.3
-rw-r--r--gn/packages/bioinformatics.scm12
-rw-r--r--gn/packages/crates-io.scm362
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)))
+