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authorEfraim Flashner2022-10-24 10:55:48 +0300
committerEfraim Flashner2022-10-24 10:55:48 +0300
commitb44f584e027d6b427dd55a42187d306a431609d9 (patch)
treeaaa9a8695affb7b13286bb5a4924fe66db6dbdba /gn/packages
parent34fa80138503c5b15a8f86ee2081c8b80b2f74cf (diff)
downloadguix-bioinformatics-b44f584e027d6b427dd55a42187d306a431609d9.tar.gz
gn: Update crates for upstream changes
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/crates-io.scm115
-rw-r--r--gn/packages/pangenome.scm15
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