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| author | Efraim Flashner | 2023-09-19 19:38:52 +0300 |
|---|---|---|
| committer | Efraim Flashner | 2023-09-19 19:43:03 +0300 |
| commit | 29839033efcc894718b1596e66bcea811da19d7a (patch) | |
| tree | ab00cb78fa89cc3e0856b137c321cd97d8afb6e1 /gn/packages/bioinformatics.scm | |
| parent | c2415bfa014892a56be9b621089a0a2ffab234f7 (diff) | |
| download | guix-bioinformatics-29839033efcc894718b1596e66bcea811da19d7a.tar.gz | |
Add pafplot
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4b37c8f..75449f3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages cpp) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) + #:use-module (gnu packages crates-graphics) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) @@ -574,6 +575,42 @@ idea is to support pangenomic applications, following the specification.") (license license:expat))) +(define-public pafplot + (let ((commit "7dda24c0aeba8556b600d53d748ae3103ec85501") + (revision "1")) + (package + (name "pafplot") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/pafplot.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04ffz0zfj4mvfxmrwgisv213fypgl02f7sim950a067pm7375g1l")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-boomphf" ,rust-boomphf-0.5) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-fnv" ,rust-fnv-1) + ("rust-lodepng" ,rust-lodepng-3) + ("rust-rgb" ,rust-rgb-0.8) + ("rust-line-drawing" ,rust-line-drawing-0.8)))) + (home-page "https://github.com/ekg/pafplot.git") + (synopsis "Base-level dotplots from PAF alignments") + (description "In the process of generating alignments between whole +genomes, we often need to understand the base-level alignment between +particular sequences. @command{pafplot} allows us to do so by rasterizing the +matches alignment set. It draws a line on a raster image to represent each +match found in a set of alignments. The resulting image provides a high-level +view of the structure of the alignments, and in consequence the homology +relationships between the sequences in consideration.") + (license license:expat)))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) |