From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add fxtract. Date: Thu, 7 Jan 2016 07:48:33 +1000 Message-ID: <568D8BB1.9040001@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------050300030203010402000501" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:49360) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aGvwk-0002CU-PI for guix-devel@gnu.org; Wed, 06 Jan 2016 16:48:47 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aGvwh-0000EB-Id for guix-devel@gnu.org; Wed, 06 Jan 2016 16:48:46 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:51457 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aGvwg-0000E3-Vb for guix-devel@gnu.org; Wed, 06 Jan 2016 16:48:43 -0500 Received: from smtp1.soe.uq.edu.au (smtp1.soe.uq.edu.au [10.138.113.40]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id u06LmZ6J017812 for ; Thu, 7 Jan 2016 07:48:36 +1000 Received: from [192.168.1.105] (static.customers.nuskope.com.au [103.25.181.216] (may be forged)) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id u06LmYXn061801 (version=TLSv1.2 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Thu, 7 Jan 2016 07:48:35 +1000 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@gnu.org" This is a multi-part message in MIME format. --------------050300030203010402000501 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Thanks in advance for review. ben --------------050300030203010402000501 Content-Type: text/x-patch; name="0001-gnu-Add-fxtract.patch" Content-Disposition: attachment; filename="0001-gnu-Add-fxtract.patch" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id u06LmZ6J017812 >From acd310d27c457139d3f2fcd2cfc1127167bf2c48 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 7 Jan 2016 07:44:58 +1000 Subject: [PATCH] gnu: Add fxtract. * gnu/packages/bioinformatics.scm (fxtract): New variable. --- gnu/packages/bioinformatics.scm | 65 +++++++++++++++++++++++++++++++++++= +++++- 1 file changed, 64 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index 76a1c17..77fe411 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright =C2=A9 2014, 2015 Ricardo Wurmus -;;; Copyright =C2=A9 2015 Ben Woodcroft +;;; Copyright =C2=A9 2015, 2016 Ben Woodcroft ;;; Copyright =C2=A9 2015 Pjotr Prins ;;; Copyright =C2=A9 2015 Andreas Enge ;;; @@ -47,6 +47,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -1436,6 +1437,68 @@ genes in incomplete assemblies or complete genomes= .") ;; GPL3+ according to private correspondense with the authors. (license license:gpl3+))) =20 +(define-public fxtract + (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) + (package + (name "fxtract") + (version "2.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/ctSkennerton/fxtract/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list + (string-append "PREFIX=3D" (assoc-ref %outputs "o= ut")) + "CC=3Dgcc") + #:test-target "fxtract_test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'copy-util + (lambda* (#:key inputs #:allow-other-keys) + (rmdir "util") + (copy-recursively (assoc-ref inputs "ctskennerton-util") = "util") + #t)) + ;; Do not use make install as this requires additional depend= encies. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out"/bin"))) + (install-file "fxtract" bin) + #t)))))) + (inputs + `(("pcre" ,pcre) + ("zlib" ,zlib))) + (native-inputs + `(("ctskennerton-util" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/util.git") + (commit util-commit))) + (file-name (string-append + "ctstennerton-util-" util-commit "-checkout")) + (sha256 + (base32 + "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))= ))) + (home-page "https://github.com/ctSkennerton/fxtract") + (synopsis "Extract sequences from FASTA and FASTQ files") + (description + "Fxtract extracts sequences from a protein or nucleotide fastx (F= ASTA +or FASTQ) file given a subsequence. It uses a simple substring search f= or +basic tasks but can change to using POSIX regular expressions, PCRE, has= h +lookups or multi-pattern searching as required. By default fxtract look= s in +the sequence of each record but can also be told to look in the header, +comment or quality sections.") + (license license:gpl3+)))) + (define-public grit (package (name "grit") --=20 2.6.3 --------------050300030203010402000501--