From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 2/2] gnu: Add EMBOSS. Date: Mon, 4 Jul 2016 13:23:24 +0200 Message-ID: <20160704112324.9531-3-ricardo.wurmus@mdc-berlin.de> References: <20160704112324.9531-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56665) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bK1yn-00020U-HT for guix-devel@gnu.org; Mon, 04 Jul 2016 07:24:00 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bK1yi-0007uv-Gs for guix-devel@gnu.org; Mon, 04 Jul 2016 07:23:56 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:46443) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bK1yi-0007ue-5M for guix-devel@gnu.org; Mon, 04 Jul 2016 07:23:52 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 5AB5C38040B for ; Mon, 4 Jul 2016 13:23:51 +0200 (CEST) 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 EofftAIrAD3t for ; Mon, 4 Jul 2016 13:23:45 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 4 Jul 2016 13:23:45 +0200 (CEST) In-Reply-To: <20160704112324.9531-1-ricardo.wurmus@mdc-berlin.de> 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 * gnu/packages/bioinformatics.scm (emboss): New variable. --- gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11784ab..05063d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -49,6 +49,8 @@ #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) + #:use-module (gnu packages gd) + #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -56,6 +58,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages pcre) + #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -70,6 +73,7 @@ #:use-module (gnu packages vim) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages xorg) #:use-module (gnu packages zip) #:use-module (srfi srfi-1)) @@ -5232,6 +5236,69 @@ datasets and the exploration of large datasets of genome intervals (e.g. genes, sequence alignments).") (license license:gpl2)))) +(define-public emboss + (package + (name "emboss") + (version "6.5.7") + (source (origin + (method url-fetch) + (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" + (version-major+minor version) ".0/" + "EMBOSS-" version ".tar.gz")) + (sha256 + (base32 + "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "--with-hpdf=" + (assoc-ref %build-inputs "libharu"))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-checks + (lambda _ + ;; The PNGDRIVER tests check for the presence of libgd, libpng + ;; and zlib, but assume that they are all found at the same + ;; prefix. + (substitute* "configure.in" + (("CHECK_PNGDRIVER") + "LIBS=\"$LIBS -lgd -lpng -lz -lm\" +AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) +AM_CONDITIONAL(AMPNG, true)")) + #t)) + (add-after 'unpack 'disable-update-check + (lambda _ + ;; At build time there is no connection to the Internet, so + ;; looking for updates will not work. + (substitute* "Makefile.am" + (("\\$\\(bindir\\)/embossupdate") "")) + #t)) + (add-before 'configure 'autogen + (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (inputs + `(("perl" ,perl) + ("libpng" ,libpng) + ("gd" ,gd) + ("libx11" ,libx11) + ("libharu" ,libharu) + ("zlib" ,zlib))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "http://emboss.sourceforge.net") + (synopsis "Molecular biology analysis suite") + (description "EMBOSS is the \"European Molecular Biology Open Software +Suite\". EMBOSS is an analysis package specially developed for the needs of +the molecular biology (e.g. EMBnet) user community. The software +automatically copes with data in a variety of formats and even allows +transparent retrieval of sequence data from the web. It also provides a +number of libraries for the development of software in the field of molecular +biology. EMBOSS also integrates a range of currently available packages and +tools for sequence analysis into a seamless whole.") + (license license:gpl2+))) + (define-public piranha ;; There is no release tarball for the latest version. The latest commit is ;; older than one year at the time of this writing. -- 2.8.4