From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: [PATCH] gnu: Add minced. Date: Mon, 15 Aug 2016 16:13:21 +0100 Message-ID: <87d1la12we.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:44762) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bZJa8-0003Jg-D8 for guix-devel@gnu.org; Mon, 15 Aug 2016 11:13:41 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bZJa3-0000z3-77 for guix-devel@gnu.org; Mon, 15 Aug 2016 11:13:39 -0400 Received: from out2-smtp.messagingengine.com ([66.111.4.26]:60428) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bZJa0-0000wy-OT for guix-devel@gnu.org; Mon, 15 Aug 2016 11:13:35 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id 89C46201B2 for ; Mon, 15 Aug 2016 11:13:23 -0400 (EDT) Received: from localhost (unknown [46.16.214.129]) by mail.messagingengine.com (Postfix) with ESMTPA id 21D68CCDCC for ; Mon, 15 Aug 2016 11:13:23 -0400 (EDT) Content-Disposition: inline; filename=0001-gnu-Add-minced.patch List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org >From 017a593d407a36ca98736b95b7413f180a7735d4 Mon Sep 17 00:00:00 2001 From: Marius Bakke 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 =C2=A9 2015 Andreas Enge ;;; Copyright =C2=A9 2016 Roel Janssen ;;; Copyright =C2=A9 2016 Efraim Flashner +;;; Copyright =C2=A9 2016 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -3117,6 +3118,56 @@ probabilistic distances of genome abundance and tetr= anucleotide frequency.") (license (license:non-copyleft "file://license.txt" "See license.txt in the distribution."))= )) =20 +(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 su= ch +as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.= ") + (license license:gpl3+))) + (define-public miso (package (name "miso") --=20 2.9.2