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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-11-11 14:44:28 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-11-11 15:39:19 +0000 |
| commit | 6be47c5bc56b4a2d3183a58d1c9fb2e0846c7f0f (patch) | |
| tree | d24c6f0b4eaa6d65e68c1d579cfd057a9d7f1b3f /gnu/packages/bioinformatics.scm | |
| parent | b8c9f061e100949f081157eb4c9a7a2299ce9187 (diff) | |
| download | guix-6be47c5bc56b4a2d3183a58d1c9fb2e0846c7f0f.tar.gz guix-6be47c5bc56b4a2d3183a58d1c9fb2e0846c7f0f.zip | |
gnu: Add circtools.
* gnu/packages/bioinformatics.scm (circtools): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae3cf01c87..13bd7b5997 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (guix hg-download) #:use-module (guix build-system ant) #:use-module (guix build-system gnu) + #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) #:use-module (guix build-system go) #:use-module (guix build-system haskell) @@ -77,6 +78,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages cran) + #:use-module (gnu packages crates-io) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages databases) @@ -1390,6 +1392,61 @@ bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.") (license license:expat))) +(define-public circtools + (package + (name "circtools") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Kevinzjy/circtools") + ;; Corresponds to tag v1.0.0 + (commit "79380de59013601021ca3b1352d6f64d2fb89646") + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0wg1s927g32k25j967kfr8l30nmr4c0p4zvy5igvy7cs6chd60lh")))) + (build-system cargo-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-writable + (lambda _ + (for-each make-file-writable (find-files ".")))) + (add-after 'unpack 'prepare-spoa-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "vendor/spoa/CMakeLists.txt" + (("find_package\\(bioparser 3.0.13 QUIET\\)") + "find_package(bioparser 3.0.13 CONFIG)") + (("find_package\\(biosoup 0.10.0 QUIET\\)") + "find_package(biosoup 0.10.0 CONFIG)") + (("GTest_FOUND") "TRUE"))))) + #:cargo-inputs + (("rust-anyhow" ,rust-anyhow-1) + ("rust-bio" ,rust-bio-0.33) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-docopt" ,rust-docopt-1) + ("rust-flate2" ,rust-flate2-1) + ("rust-indicatif" ,rust-indicatif-0.15) + ("rust-libc" ,rust-libc-0.2) + ("rust-serde" ,rust-serde-1) + ("rust-seq-io" ,rust-seq-io-0.3)))) + (inputs + `(("bioparser" ,bioparser) + ("biosoup" ,biosoup))) + (native-inputs + `(("cmake" ,cmake) + ("pkg-config" ,pkg-config) + ("googletest" ,googletest))) + (home-page "https://github.com/Kevinzjy/circtools") + (synopsis "Accelerating functions in CIRI toolkit") + (description "This package provides accelerated functions for the CIRI +toolkit. It also provides the @code{ccs} executable to scan for circular +consensus sequences.") + (license license:expat))) + (define-public ciri-long (package (name "ciri-long") |