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[82.242.148.1]) by smtp.gmail.com with ESMTPSA id q187sm9454774wma.41.2020.04.17.15.24.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 17 Apr 2020 15:24:55 -0700 (PDT) From: Vincent Legoll Date: Sat, 18 Apr 2020 00:24:44 +0200 Message-Id: <20200417222444.11115-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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")