From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:58189) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jPZQx-0004hA-Ji for guix-patches@gnu.org; Fri, 17 Apr 2020 18:26:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1jPZQw-0008Si-97 for guix-patches@gnu.org; Fri, 17 Apr 2020 18:26:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:58537) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1jPZQw-0008Ry-4r for guix-patches@gnu.org; Fri, 17 Apr 2020 18:26:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jPZQw-0004RF-1l for guix-patches@gnu.org; Fri, 17 Apr 2020 18:26:02 -0400 Subject: [bug#40691] [PATCH] gnu: Add gromacs. References: In-Reply-To: Resent-Message-ID: From: Vincent Legoll Date: Sat, 18 Apr 2020 00:24:44 +0200 Message-Id: <20200417222444.11115-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 40691@debbugs.gnu.org Cc: Vincent Legoll * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..f0fca30dd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,6 +786,44 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on"))) + (native-inputs + `(("doxygen" ,doxygen) ; need dot + ("python-sphinx" ,python-sphinx))) ; problem reported by cmake + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0