Subject: Re: [bug#40691] [PATCH v2 1/1] gnu: Add gromacs.

From: Vincent Legoll <[email-masked]>
Date: Tue, 21 Apr 2020 00:15:05 +0200

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

>From 650247f97a56f2967d068ee8b1911fae6412ce4d Mon Sep 17 00:00:00 2001
From: Vincent Legoll <[email-masked]>
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 <[email-masked]>
 ;;; Copyright © 2020 Björn Höfling <[email-masked]>
 ;;; Copyright © 2020 Jakub Kądziołka <[email-masked]>
+;;; Copyright © 2020 Vincent Legoll <[email-masked]>
 ;;;
 ;;; 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