From: Vincent Legoll <vincent.legoll@gmail.com>
To: "Ludovic Courtès" <ludo@gnu.org>
Cc: 40691@debbugs.gnu.org
Subject: [bug#40691] [PATCH v2 1/1] gnu: Add gromacs.
Date: Tue, 21 Apr 2020 00:15:05 +0200 [thread overview]
Message-ID: <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> (raw)
In-Reply-To: <87k12b15ki.fsf@gnu.org>
[-- Attachment #1: Type: text/plain, Size: 989 bytes --]
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
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From 650247f97a56f2967d068ee8b1911fae6412ce4d Mon Sep 17 00:00:00 2001
From: Vincent Legoll <vincent.legoll@gmail.com>
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 <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;;
;;; 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
next prev parent reply other threads:[~2020-04-20 22:16 UTC|newest]
Thread overview: 30+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-04-17 22:22 [bug#40691] [PATCH 0/1] gnu: Add gromacs Vincent Legoll
2020-04-17 22:24 ` [bug#40691] [PATCH] " Vincent Legoll
2020-04-17 22:48 ` [bug#40691] gromacs - WIP, submitted Vincent Legoll
2020-04-19 22:19 ` [bug#40691] [PATCH 0/1] gnu: Add gromacs Ludovic Courtès
2020-04-20 22:15 ` Vincent Legoll [this message]
2020-04-22 15:38 ` [bug#40691] [PATCH v2 1/1] " Ludovic Courtès
2020-04-23 13:07 ` [bug#40691] [PATCH v3 " Vincent Legoll
2020-04-23 19:52 ` Ludovic Courtès
2020-05-01 22:30 ` Vincent Legoll
2020-05-02 13:35 ` Ludovic Courtès
2020-05-02 13:46 ` [bug#40691] [PATCH v4 0/3] gnu: Add gromacs, tng & lmfit Vincent Legoll
2020-05-03 10:39 ` Ludovic Courtès
2020-05-03 22:31 ` [bug#40691] [PATCH v6 " Vincent Legoll
2020-05-04 8:40 ` bug#40691: " Ludovic Courtès
2020-05-02 13:48 ` [bug#40691] [PATCH 1/3] gnu: Add tng Vincent Legoll
2020-05-02 13:48 ` [bug#40691] [PATCH 2/3] gnu: Add lmfit Vincent Legoll
2020-05-02 13:48 ` [bug#40691] [PATCH 3/3] gnu: Add gromacs Vincent Legoll
2020-05-02 13:53 ` [bug#40691] [PATCH v4 0/3]: " Vincent Legoll
2020-05-02 16:43 ` [bug#40691] [PATCH 1/3] gnu: Add tng Vincent Legoll
2020-05-02 16:43 ` [bug#40691] [PATCH 2/3] gnu: Add lmfit Vincent Legoll
2020-05-03 10:43 ` Ludovic Courtès
2020-05-02 16:43 ` [bug#40691] [PATCH 3/3] gnu: Add gromacs Vincent Legoll
2020-05-03 10:46 ` Ludovic Courtès
2020-05-03 10:41 ` [bug#40691] [PATCH 1/3] gnu: Add tng Ludovic Courtès
2020-05-03 22:32 ` Vincent Legoll
2020-05-03 22:32 ` [bug#40691] [PATCH 2/3] gnu: Add lmfit Vincent Legoll
2020-05-03 22:32 ` [bug#40691] [PATCH 3/3] gnu: Add gromacs Vincent Legoll
2020-05-03 22:39 ` Vincent Legoll
2020-05-03 22:39 ` [bug#40691] [PATCH] " Vincent Legoll
2020-05-05 21:27 ` [bug#40691] Upstream patches are being merged Vincent Legoll
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