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authorMarius Bakke <mbakke@fastmail.com>2016-08-15 16:06:37 +0100
committerBen Woodcroft <donttrustben@gmail.com>2016-08-17 20:56:21 +1000
commit318c0aee1ec2f33e4dfb7f4daa4a67cfcbe78629 (patch)
tree2567799dd476b46ffc92df5448336b386636af2d
parentd80a71eb9b923025c4179e7edc8d26ffd70cbe44 (diff)
downloadpatches-318c0aee1ec2f33e4dfb7f4daa4a67cfcbe78629.tar
patches-318c0aee1ec2f33e4dfb7f4daa4a67cfcbe78629.tar.gz
gnu: Add minced.
* gnu/packages/bioinformatics.scm (minced): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
-rw-r--r--gnu/packages/bioinformatics.scm58
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")