From 017a593d407a36ca98736b95b7413f180a7735d4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 15 Aug 2016 16:06:37 +0100
Subject: [PATCH] gnu: Add minced.

* gnu/packages/bioinformatics.scm (minced): New variable.
---
 gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a3f0d81..e76dc4d 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.
 ;;;
@@ -3117,6 +3118,56 @@ 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"))))
+         (add-before 'install 'qualify-java-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "minced"
+               ;; Set full path to java binary in wrapper script.
+               (("^java") (string-append (assoc-ref inputs "jre")
+                                         "/bin/java")))))
+         (replace 'install
+           ;; No install target.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         (list "minced" "minced.jar"))))))))
+    (native-inputs
+     `(("jdk", icedtea "jdk")))
+    (inputs
+     `(("jre", icedtea)))
+    (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 full genomes or environmental datasets such
+as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.")
+    (license license:gpl3+)))
+
 (define-public miso
   (package
     (name "miso")
-- 
2.9.2