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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd69e39bcc..b31cf7cfe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,6 +41,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) #:use-module (gnu packages base) + #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages compression) @@ -3118,6 +3120,62 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (license (license:non-copyleft "file://license.txt" "See license.txt in the distribution.")))) +(define-public minced + (package + (name "minced") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/ctSkennerton/minced/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'check 'fix-test + (lambda _ + ;; Fix test for latest version. + (substitute* "t/Aquifex_aeolicus_VF5.expected" + (("minced:0.1.6") "minced:0.2.0")) + #t)) + (replace 'install ; No install target. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (wrapper (string-append bin "/minced"))) + ;; Minced comes with a wrapper script that tries to figure out where + ;; it is located before running the JAR. Since these paths are known + ;; to us, we build our own wrapper to avoid coreutils dependency. + (install-file "minced.jar" bin) + (with-output-to-file wrapper + (lambda _ + (display + (string-append + "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" + (assoc-ref inputs "jre") "/bin/java -jar " + bin "/minced.jar \"$@\"\n")))) + (chmod wrapper #o555))))))) + (native-inputs + `(("jdk" ,icedtea "jdk"))) + (inputs + `(("bash" ,bash) + ("jre" ,icedtea "out"))) + (home-page "https://github.com/ctSkennerton/minced") + (synopsis "Mining CRISPRs in Environmental Datasets") + (description + "MinCED is a program to find Clustered Regularly Interspaced Short +Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for +unassembled metagenomic reads, but is mainly designed for full genomes and +assembled metagenomic sequence.") + (license license:gpl3+))) + (define-public miso (package (name "miso") |