From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add cutadapt. Date: Fri, 20 Mar 2015 16:18:38 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52624) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYyhG-0003Mw-GT for guix-devel@gnu.org; Fri, 20 Mar 2015 11:18:51 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YYyhC-00019C-AI for guix-devel@gnu.org; Fri, 20 Mar 2015 11:18:50 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:48165) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYyhB-00018k-UC for guix-devel@gnu.org; Fri, 20 Mar 2015 11:18:46 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 4195A380EC8 for ; Fri, 20 Mar 2015 16:18:44 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id KEKmCWiiYy0i for ; Fri, 20 Mar 2015 16:18:38 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 20 Mar 2015 16:18:38 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-cutadapt.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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel >From 18a14112b6e22248638d2b34e1c1b935e1bcd343 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Mar 2015 16:17:55 +0100 Subject: [PATCH] gnu: Add cutadapt. * gnu/packages/bioinformatics.scm (cutadapt): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 46ce4f4..5805e42 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ (define-module (gnu packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) @@ -405,6 +406,45 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public cutadapt + (package + (name "cutadapt") + (version "1.8") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marcelm/cutadapt/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) + (build-system python-build-system) + (arguments + ;; tests must be run after install + `(#:phases (alist-cons-after + 'install 'check + (lambda* (#:key outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + ,(version-major+minor (package-version python)) + "/site-packages")) + (zero? (system* "nosetests" "-P" "tests"))) + (alist-delete 'check %standard-phases)))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://code.google.com/p/cutadapt/") + (synopsis "Remove adapter sequences from nucleotide sequencing reads") + (description + "Cutadapt finds and removes adapter sequences, primers, poly-A tails and +other types of unwanted sequence from high-throughput sequencing reads.") + (license license:expat))) + (define-public flexbar (package (name "flexbar") -- 2.1.0