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Change-Id: I38f984b308db0a3a5756852cd89de25ae0875f76 --- gnu/packages/bioinformatics.scm | 68 +++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) base-commit: 580d77d0fb12448ef1621699cc0c56e787e2aadb diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cecd94bbb7..d12ec9a249 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -26,6 +26,7 @@ ;;; Copyright © 2022, 2023 Navid Afkhami ;;; Copyright © 2022 Antero Mejr ;;; Copyright © 2024 Alexis Simon +;;; Copyright © 2024 gemmaro ;;; ;;; This file is part of GNU Guix. ;;; @@ -172,6 +173,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages wget) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) + #:use-module (gnu packages xdisorg) #:use-module (guix platform) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) @@ -22617,6 +22619,72 @@ (define-public hh-suite based on the pairwise alignment of hidden Markov models (HMMs).") (license license:gpl3+))) +(define-public mashmap + (package + (name "mashmap") + (version "3.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marbl/MashMap") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0iqgcx5jk6asihdvzv2sa5v373y9k9fsd2a2in25ragil8z8nckp")))) + (build-system cmake-build-system) + (arguments + (list + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((gnuplot (string-append (assoc-ref inputs + "gnuplot") + "/bin/gnuplot")) + (xclip (string-append (assoc-ref inputs "xclip") + "/bin/xclip"))) + (substitute* "scripts/generateDotPlot" + (("gnuplot --version") + (string-append gnuplot " --version")) + (("my \\$cmd = \"gnuplot\";") + (string-append "my $cmd = \"" gnuplot "\";")) + (("xclip -o") + (string-append xclip " -o")))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (begin + (invoke "../build/bin/mashmap" + "-r" "../source/data/scerevisiae8.fa.gz" + "-q" "../source/data/scerevisiae8.fa.gz" + "--pi" "95" + "-n" "1" + "-Y" "#" + "-o" "scerevisiae8.paf") + (invoke "../source/scripts/test.sh" + "../source/data/scerevisiae8.fa.gz.fai" + "scerevisiae8.paf" "0.92"))))) + (add-after 'install 'install-script + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "../source/scripts/generateDotPlot" + (string-append out "/share/mashmap")))))))) + (native-inputs (list bedtools util-linux)) + (inputs (list gsl + zlib + htslib + perl + gnuplot + xclip)) + (home-page "https://github.com/marbl/MashMap") + (synopsis "Fast approximate aligner for long DNA sequences") + (description + "MashMap implements a fast and approximate algorithm for computing +local alignment boundaries between long DNA sequences. It can be +useful for mapping genome assembly or long reads (PacBio/ONT) to +reference genome(s).") + (license license:public-domain))) + (define-public wfmash (package (name "wfmash")