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gfaffix.scm
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(define-module (gfaffix)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system cargo)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages crates-graphics)
#:use-module (gnu packages rust))
(define-public gfaffix
(package
(name "gfaffix")
(version "0.1.3")
(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 "1biss5qv6ag1dfkn1nspwd528hpzgn8i4jydvbv2z7yv7sc685rh"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "Cargo.toml"
(("^handlegraph.*") "handlegraph = \"0.7\"\n"))))))
(build-system cargo-build-system)
(arguments
`(#: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)
("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)
(let ((handlebar-version ,(package-version rust-handlegraph-0.7)))
(substitute* "Cargo.toml"
(("\"0.7\"")
(string-append "{ version = \"" handlebar-version "\" }")))))))))
(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)))
(define-public rust-handlegraph-0.7
(package
(inherit rust-handlegraph-0.3)
(name "rust-handlegraph")
(version "0.7.0-alpha.9")
(source
(origin
(method url-fetch)
(uri (crate-uri "handlegraph" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs"))))
(arguments
`(#: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-handlegraph-0.7
(package
(inherit rust-handlegraph-0.3)
(name "rust-handlegraph")
(version "0.7.0-alpha.9")
(source
(origin
(method url-fetch)
(uri (crate-uri "handlegraph" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs"))))
(arguments
`(#: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-clap-for-jrep
(package
(name "rust-clap")
(version "2.33.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "clap" version))
(file-name
(string-append name "-" version ".tar.gz"))
(sha256
(base32
"1nf6ld3bims1n5vfzhkvcb55pdzh04bbhzf8nil5vvw05nxzarsh"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-atty" ,rust-atty-0.2)
("rust-bitflags" ,rust-bitflags-1)
("rust-clap-derive" ,rust-clap-derive-3)
("rust-indexmap" ,rust-indexmap-1)
("rust-os-str-bytes" ,rust-os-str-bytes-2)
("rust-strsim" ,rust-strsim-0.10)
("rust-termcolor" ,rust-termcolor-1)
("rust-ansi-term" ,rust-ansi-term-0.11)
("rust-terminal-size" ,rust-terminal-size-0.1)
("rust-textwrap" ,rust-textwrap-0.12)
("rust-unicode-width" ,rust-unicode-width-0.1)
("rust-vec-map" ,rust-vec-map-0.8)
("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-version-sync" ,rust-version-sync-0.8))))
(home-page "https://clap.rs/")
(synopsis "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 jrep
(package
(name "jrep")
(version "0.1.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/joshua-laughner/jrep")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0syvlc93w26v856hp5l8ik615dfrvax6hdfzw5kqhaww3siqjaj9"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-clap" ,rust-clap-for-jrep)
("rust-exitcode" ,rust-exitcode-1)
("rust-term" ,rust-term-0.7)
("rust-regex" ,rust-regex-1)
("rust-serde" ,rust-serde-1)
("rust-serde-json" ,rust-serde-json-1))))
(home-page "https://github.com/joshua-laughner/jrep/")
(synopsis "grep for Jupyter notebooks")
(description
"@code{jrep} is @code{grep} for Jupyter notebooks. It is a command line
program that can search across multiple notebooks for specific text,
but limit itself to certain types of cells, source text, output data,
or any combination.")
(license license:gpl3+)))
(define-public notebook-tools
(let ((commit "a9db1f4f90f6df72d28bf1235ca16b988d7b86be")
(revision "0"))
(package
(name "notebook-tools")
(version commit)
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/CADLabs/notebook-tools")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0mmvqjfcsa6fq12rpay9w6ra1q8ijhmm1raqzi4d70y7wsbd20lw"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-clap" ,rust-clap-3)
("rust-exitcode" ,rust-exitcode-1)
("rust-term" ,rust-term-0.7)
("rust-regex" ,rust-regex-1)
("rust-serde" ,rust-serde-1)
("rust-serde-json" ,rust-serde-json-1))))
(home-page "https://github.com/CADLabs/notebook-tools")
(synopsis "Rust CLI tools for manipulation of Jupyter Notebooks")
(description "Rust CLI tools for manipulation of Jupyter Notebooks.")
(license #f)))) ; There is no license.
;; replace fields with those from upstream
(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
`(#: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))))
;; ready to upstream, WITH rust-clap-derive
;; replace fields with those from upstream.
(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-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
`(#:skip-build? #t ; Not all inputs packaged
;#: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
`(;#:skip-build? #t ; Not all inputs at correct versions?
;#:tests? #f ; Skip tests for now
#: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-toml-edit-0.12
(package
(name "rust-toml-edit")
(version "0.12.6")
(source
(origin
(method url-fetch)
(uri (crate-uri "toml-edit" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0wx4wd849bmkqj0gdi041gmpfpvlyhy2ha4zpin69yw9d9npl8cl"))))
(build-system cargo-build-system)
(arguments
`(;#:skip-build? #t ; Not all inputs packaged
;#:tests? #f ; Skip tests for now
#:cargo-inputs
(("rust-combine" ,rust-combine-4)
("rust-indexmap" ,rust-indexmap-1)
("rust-itertools" ,rust-itertools-0.10)
("rust-kstring" ,rust-kstring-1)
("rust-serde" ,rust-serde-1))
#:cargo-development-inputs
(("rust-criterion" ,rust-criterion-0.3)
;("rust-fs-snapshot" ,rust-fs-snapshot-0.1)
;("rust-pretty-assertions" ,rust-pretty-assertions-1)
("rust-serde-json" ,rust-serde-json-1)
("rust-toml" ,rust-toml-0.5)
;("rust-toml-test-harness" ,rust-toml-test-harness-0.3)
)))
(home-page "https://github.com/ordian/toml_edit")
(synopsis "Yet another format-preserving TOML parser.")
(description "Yet another format-preserving TOML parser.")
(license (list license:expat license:asl2.0))))