From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: Re: [PATCH] gnu: Add minced. Date: Tue, 16 Aug 2016 13:49:23 +0100 Message-ID: <87wpjgzxnw.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> References: <87d1la12we.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> <72c865bb-0ce4-4c51-6029-d8398711135a@uq.edu.au> <87zioczycq.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:42142) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bZdoK-0000Ji-8w for guix-devel@gnu.org; Tue, 16 Aug 2016 08:49:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bZdoF-0001a6-Uz for guix-devel@gnu.org; Tue, 16 Aug 2016 08:49:40 -0400 Received: from out2-smtp.messagingengine.com ([66.111.4.26]:51282) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bZdoD-0001Zc-KB for guix-devel@gnu.org; Tue, 16 Aug 2016 08:49:35 -0400 In-Reply-To: <87zioczycq.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> 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: Ben Woodcroft , guix-devel@gnu.org --=-=-= Content-Type: text/plain > Please find updated patch below. Thanks for the feedback! Ugh. Missed a commit when squashing. Here is the final patch: --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-Add-minced.patch Content-Transfer-Encoding: quoted-printable >From bb50f5c0d960625483e8db15a270a7f17d5d2d9c 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 | 58 +++++++++++++++++++++++++++++++++++++= ++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index dd69e39..6a27e06 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. ;;; @@ -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 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")) + #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 depen= dency. + (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))) + (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 unassem= bled +metagenomic reads, but is mainly designed for full genomes and assembled +metagenomic sequence.") + (license license:gpl3+))) + (define-public miso (package (name "miso") --=20 2.9.2 --=-=-=--