From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:49744) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jQehv-0002og-H3 for guix-patches@gnu.org; Mon, 20 Apr 2020 18:16:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jQehv-0007B1-0f for guix-patches@gnu.org; Mon, 20 Apr 2020 18:16:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:37074) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jQehu-0007Av-KP for guix-patches@gnu.org; Mon, 20 Apr 2020 18:16:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jQehu-0008NH-Ef for guix-patches@gnu.org; Mon, 20 Apr 2020 18:16:02 -0400 Subject: [bug#40691] [PATCH v2 1/1] gnu: Add gromacs. Resent-Message-ID: References: <87k12b15ki.fsf@gnu.org> From: Vincent Legoll Message-ID: <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> Date: Tue, 21 Apr 2020 00:15:05 +0200 MIME-Version: 1.0 In-Reply-To: <87k12b15ki.fsf@gnu.org> Content-Type: multipart/mixed; boundary="------------96D85335278C67436673ED76" Content-Language: en-US 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: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org This is a multi-part message in MIME format. --------------96D85335278C67436673ED76 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hello, On 20/04/2020 00:19, Ludovic Courtès wrote: > Could you add a comment explaining the reason for this flag? Done, it'to build test executables. >> problems reported by cmake: >> >> -- Found Doxygen: >> /gnu/store/k6albjaxkybsgshqyw6g44f5hz75l7q6-doxygen-1.8.15/bin/doxygen >> (found version "1.8.15") found components: doxygen missing >> components: dot > > Perhaps add ‘graphviz’ as a native input? Yep, that fixed it >> -- Could NOT find Sphinx: Found unsuitable version "-real 2.3.1", but >> required is at least "1.6.1" (found >> /gnu/store/anyhb84x3mvyp11sbhmdnicbsa42m3x0-python-sphinx-2.3.1/bin/sphinx-build) > > Oh, looks like it’s looking at argv[0] and the script is wrapped. :-/ > Can you somehow for CMake to think it’s fine, either with a flag or by > skipping the relevant check in ‘CMakeLists.txt’? Done, passing the version to cmake & adding pygments to inputs made it pass. Thanks for the help How's the attached v2 ? -- Vincent Legoll --------------96D85335278C67436673ED76 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-gromacs.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-gromacs.patch" >From 650247f97a56f2967d068ee8b1911fae6412ce4d Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sat, 18 Apr 2020 00:14:56 +0200 Subject: [PATCH] gnu: Add gromacs. * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..1b643e29c8 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. ;;; @@ -79,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -785,6 +787,51 @@ 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" ; Needed to run tests + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))))) + (native-inputs + `(("doxygen" ,doxygen) + ("graphviz" ,graphviz) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (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 --------------96D85335278C67436673ED76--