5ab0cbd0f1
* gnu/packages/python-xyz.scm (python2-numpy): Delete variable. (python2-numpy-1.8): Likewise. (python-numpy)[properties]: Delete field. * gnu/packages/maths.scm (flann): Delete comment. * gnu/packages/chemistry.scm (with-numpy-1.8): Delete procedure.
569 lines
23 KiB
Scheme
569 lines
23 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
|
|
;;; Copyright © 2018, 2021 Kei Kebreau <kkebreau@posteo.net>
|
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;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
|
|
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
|
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
|
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
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;;;
|
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;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages chemistry)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix utils)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (guix download)
|
|
#:use-module (guix git-download)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages backup)
|
|
#:use-module (gnu packages boost)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages documentation)
|
|
#:use-module (gnu packages fontutils)
|
|
#:use-module (gnu packages gl)
|
|
#:use-module (gnu packages graphviz)
|
|
#:use-module (gnu packages gv)
|
|
#:use-module (gnu packages image)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages mpi)
|
|
#:use-module (gnu packages perl)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages qt)
|
|
#:use-module (gnu packages serialization)
|
|
#:use-module (gnu packages sphinx)
|
|
#:use-module (gnu packages xml)
|
|
#:use-module (guix build-system cmake)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system python))
|
|
|
|
(define-public avogadrolibs
|
|
(package
|
|
(name "avogadrolibs")
|
|
(version "1.93.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/OpenChemistry/avogadrolibs")
|
|
(commit version)))
|
|
(sha256
|
|
(base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
(list eigen
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|
mmtf-cpp
|
|
msgpack
|
|
googletest
|
|
pkg-config
|
|
pybind11))
|
|
(inputs
|
|
(list glew
|
|
libarchive
|
|
libmsym
|
|
molequeue
|
|
python
|
|
spglib
|
|
qtbase-5))
|
|
(arguments
|
|
'(#:configure-flags (list "-DENABLE_TESTING=ON"
|
|
(string-append "-DSPGLIB_INCLUDE_DIR="
|
|
(assoc-ref %build-inputs "spglib")
|
|
"/include"))))
|
|
(home-page "https://www.openchemistry.org/projects/avogadro2/")
|
|
(synopsis "Libraries for chemistry, bioinformatics, and related areas")
|
|
(description
|
|
"Avogadro libraries provide 3D rendering, visualization, analysis and data
|
|
processing useful in computational chemistry, molecular modeling,
|
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bioinformatics, materials science, and related areas.")
|
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(license license:bsd-3)))
|
|
|
|
(define-public avogadro2
|
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(package
|
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(name "avogadro2")
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(version "1.93.0")
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(source
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(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/OpenChemistry/avogadroapp")
|
|
(commit version)))
|
|
(sha256
|
|
(base32
|
|
"1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
(list eigen pkg-config))
|
|
(inputs
|
|
(list avogadrolibs hdf5 molequeue qtbase-5))
|
|
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
|
|
(arguments
|
|
'(#:tests? #f))
|
|
(home-page "https://www.openchemistry.org/projects/avogadro2/")
|
|
(synopsis "Advanced molecule editor")
|
|
(description
|
|
"Avogadro 2 is an advanced molecule editor and visualizer designed for use
|
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in computational chemistry, molecular modeling, bioinformatics, materials
|
|
science, and related areas. It offers flexible high quality rendering and a
|
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powerful plugin architecture.")
|
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(license license:bsd-3)))
|
|
|
|
(define-public inchi
|
|
(package
|
|
(name "inchi")
|
|
;; Update the inchi-doc native input when updating inchi.
|
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(version "1.06")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.inchi-trust.org/download/"
|
|
(string-join (string-split version #\.) "")
|
|
"/INCHI-1-SRC.zip"))
|
|
(sha256
|
|
(base32
|
|
"1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
|
|
(file-name (string-append name "-" version ".zip"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
'(#:tests? #f ; no check target
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure) ; no configure script
|
|
(add-before 'build 'chdir-to-build-directory
|
|
(lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
|
|
(add-after 'build 'build-library
|
|
(lambda _
|
|
(chdir "../../../INCHI_API/libinchi/gcc")
|
|
(invoke "make")))
|
|
(replace 'install
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin"))
|
|
(doc (string-append out "/share/doc/inchi"))
|
|
(include-dir (string-append out "/include/inchi"))
|
|
(lib (string-append out "/lib/inchi"))
|
|
(inchi-doc (assoc-ref inputs "inchi-doc"))
|
|
(unzip (search-input-file inputs "/bin/unzip")))
|
|
(chdir "../../..")
|
|
;; Install binary.
|
|
(with-directory-excursion "INCHI_EXE/bin/Linux"
|
|
(rename-file "inchi-1" "inchi")
|
|
(install-file "inchi" bin))
|
|
;; Install libraries.
|
|
(with-directory-excursion "INCHI_API/bin/Linux"
|
|
(for-each (lambda (file)
|
|
(install-file file lib))
|
|
(find-files "." "libinchi\\.so\\.1\\.*")))
|
|
;; Install header files.
|
|
(with-directory-excursion "INCHI_BASE/src"
|
|
(for-each (lambda (file)
|
|
(install-file file include-dir))
|
|
(find-files "." "\\.h$")))
|
|
;; Install documentation.
|
|
(mkdir-p doc)
|
|
(invoke unzip "-j" "-d" doc inchi-doc)
|
|
#t))))))
|
|
(native-inputs
|
|
`(("unzip" ,unzip)
|
|
("inchi-doc"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.inchi-trust.org/download/"
|
|
(string-join (string-split version #\.) "")
|
|
"/INCHI-1-DOC.zip"))
|
|
(sha256
|
|
(base32
|
|
"1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
|
|
(file-name (string-append name "-" version ".zip"))))))
|
|
(home-page "https://www.inchi-trust.org")
|
|
(synopsis "Utility for manipulating machine-readable chemical structures")
|
|
(description
|
|
"The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
|
|
chemical structures into machine-readable strings of information. InChIs are
|
|
unique to the compound they describe and can encode absolute stereochemistry
|
|
making chemicals and chemistry machine-readable and discoverable. A simple
|
|
analogy is that InChI is the bar-code for chemistry and chemical structures.")
|
|
(license (license:non-copyleft
|
|
"file://LICENCE"
|
|
"See LICENCE in the distribution."))))
|
|
|
|
(define-public libmsym
|
|
(package
|
|
(name "libmsym")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/mcodev31/libmsym")
|
|
(commit (string-append "v" version))))
|
|
(sha256
|
|
(base32
|
|
"0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
|
|
#:tests? #f)) ; no check target
|
|
(home-page "https://github.com/mcodev31/libmsym")
|
|
(synopsis "C library dealing with point group symmetry in molecules")
|
|
(description "libmsym is a C library dealing with point group symmetry in
|
|
molecules.")
|
|
(license license:expat)))
|
|
|
|
(define-public mmtf-cpp
|
|
(package
|
|
(name "mmtf-cpp")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/rcsb/mmtf-cpp")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
|
|
(build-system cmake-build-system)
|
|
;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
|
|
(arguments
|
|
'(#:tests? #f))
|
|
(home-page "https://mmtf.rcsb.org/")
|
|
(synopsis "C++ API for the Macromolecular Transmission Format")
|
|
(description "This package is a library for the
|
|
@acronym{MMTF,macromolecular transmission format}, a binary encoding of
|
|
biological structures.")
|
|
(license license:expat)))
|
|
|
|
(define-public molequeue
|
|
(package
|
|
(name "molequeue")
|
|
(version "0.9.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://github.com/OpenChemistry/molequeue/"
|
|
"releases/download/" version "/molequeue-"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
|
|
(build-system cmake-build-system)
|
|
(inputs
|
|
(list qtbase-5))
|
|
(arguments
|
|
'(#:configure-flags '("-DENABLE_TESTING=ON")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-tests
|
|
(lambda _
|
|
;; TODO: Fix/enable the failing message and clientserver tests.
|
|
;; In the message test, the floating-point value "5.36893473232" on
|
|
;; line 165 of molequeue/app/testing/messagetest.cpp should
|
|
;; (apparently) be truncated, but it is not.
|
|
(substitute* "molequeue/app/testing/messagetest.cpp"
|
|
(("5\\.36893473232") "5.36893"))
|
|
;; It is unclear why the clientserver test fails, so it is
|
|
;; completely disabled.
|
|
(substitute* "molequeue/app/testing/CMakeLists.txt"
|
|
((".*clientserver.*") ""))
|
|
#t))
|
|
(add-before 'check 'set-display
|
|
(lambda _
|
|
;; Make Qt render "offscreen" for the sake of tests.
|
|
(setenv "QT_QPA_PLATFORM" "offscreen")
|
|
#t)))))
|
|
(home-page "https://www.openchemistry.org/projects/molequeue/")
|
|
(synopsis "Application for coordinating computational jobs")
|
|
(description "MoleQueue is a system-tray resident desktop application for
|
|
abstracting, managing, and coordinating the execution of tasks both locally and
|
|
on remote computational resources. Users can set up local and remote queues
|
|
that describe where the task will be executed. Each queue can have programs,
|
|
with templates to facilitate the execution of the program. Input files can be
|
|
staged, and output files collected using a standard interface.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public tng
|
|
(package
|
|
(name "tng")
|
|
(version "1.8.2")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/gromacs/tng")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
|
|
(build-system cmake-build-system)
|
|
(inputs
|
|
(list zlib))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'remove-bundled-zlib
|
|
(lambda _
|
|
(delete-file-recursively "external")
|
|
#t))
|
|
(replace 'check
|
|
(lambda _
|
|
(invoke "../build/bin/tests/tng_testing")
|
|
#t)))))
|
|
(home-page "https://github.com/gromacs/tng")
|
|
(synopsis "Trajectory Next Generation binary format manipulation library")
|
|
(description "TRAJNG (Trajectory next generation) is a program library for
|
|
handling molecular dynamics (MD) trajectories. It can store coordinates, and
|
|
optionally velocities and the H-matrix. Coordinates and velocities are
|
|
stored with user-specified precision.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public gromacs
|
|
(package
|
|
(name "gromacs")
|
|
(version "2020.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
|
|
;; require fixing `testutils' code. See patch header for more info
|
|
(patches (search-patches "gromacs-tinyxml2.patch"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
|
|
;; Unbundling
|
|
"-DGMX_USE_LMFIT=EXTERNAL"
|
|
"-DGMX_BUILD_OWN_FFTW=off"
|
|
"-DGMX_EXTERNAL_BLAS=on"
|
|
"-DGMX_EXTERNAL_LAPACK=on"
|
|
"-DGMX_EXTERNAL_TNG=on"
|
|
"-DGMX_EXTERNAL_ZLIB=on"
|
|
"-DGMX_EXTERNAL_TINYXML2=on"
|
|
(string-append "-DTinyXML2_DIR="
|
|
(assoc-ref %build-inputs "tinyxml2"))
|
|
;; 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)))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'fixes
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; Still bundled: part of gromacs, source behind registration
|
|
;; but free software anyways
|
|
;;(delete-file-recursively "src/external/vmd_molfile")
|
|
;; Still bundled: threads-based OpenMPI-compatible fallback
|
|
;; designed to be bundled like that
|
|
;;(delete-file-recursively "src/external/thread_mpi")
|
|
;; Unbundling
|
|
(delete-file-recursively "src/external/lmfit")
|
|
(delete-file-recursively "src/external/clFFT")
|
|
(delete-file-recursively "src/external/fftpack")
|
|
(delete-file-recursively "src/external/build-fftw")
|
|
(delete-file-recursively "src/external/tng_io")
|
|
(delete-file-recursively "src/external/tinyxml2")
|
|
(delete-file-recursively "src/external/googletest")
|
|
(copy-recursively (assoc-ref inputs "googletest-source")
|
|
"src/external/googletest")
|
|
;; This test warns about the build host hardware, disable
|
|
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
|
|
(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
|
|
"void __guix_disabled()"))
|
|
#t)))))
|
|
(native-inputs
|
|
`(("doxygen" ,doxygen)
|
|
("googletest-source" ,(package-source googletest))
|
|
("graphviz" ,graphviz)
|
|
("pkg-config" ,pkg-config)
|
|
("python" ,python)
|
|
("python-pygments" ,python-pygments)
|
|
("python-sphinx" ,python-sphinx)))
|
|
(inputs
|
|
(list fftwf
|
|
`(,hwloc-2 "lib")
|
|
lmfit
|
|
openblas
|
|
perl
|
|
tinyxml2
|
|
tng))
|
|
(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 openbabel
|
|
(package
|
|
(name "openbabel")
|
|
(version "3.1.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://github.com/openbabel/openbabel/"
|
|
"releases/download/openbabel-"
|
|
(string-replace-substring version "." "-")
|
|
"/openbabel-" version "-source.tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"0s0f4zib8vshfaywsr5bjjz55jwsg6yiz2qw4i5jm8wysn0q7v56"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(;; FIXME: Disable tests on i686 to work around
|
|
;; https://github.com/openbabel/openbabel/issues/2041.
|
|
#:tests? ,(or (%current-target-system)
|
|
(not (string=? "i686-linux" (%current-system))))
|
|
#:configure-flags
|
|
(list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
|
|
(string-append "-DINCHI_LIBRARY="
|
|
(assoc-ref %build-inputs "inchi")
|
|
"/lib/inchi/libinchi.so.1")
|
|
(string-append "-DINCHI_INCLUDE_DIR="
|
|
(assoc-ref %build-inputs "inchi") "/include/inchi"))
|
|
#:test-target "test"))
|
|
(native-inputs
|
|
(list pkg-config))
|
|
(inputs
|
|
(list eigen inchi libxml2 zlib))
|
|
(home-page "http://openbabel.org/wiki/Main_Page")
|
|
(synopsis "Chemistry data manipulation toolbox")
|
|
(description
|
|
"Open Babel is a chemical toolbox designed to speak the many languages of
|
|
chemical data. It's a collaborative project allowing anyone to search, convert,
|
|
analyze, or store data from molecular modeling, chemistry, solid-state
|
|
materials, biochemistry, or related areas.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public spglib
|
|
(package
|
|
(name "spglib")
|
|
(version "1.16.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/spglib/spglib")
|
|
(commit (string-append "v" version))))
|
|
(sha256
|
|
(base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
|
|
(file-name (git-file-name name version))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:test-target "check"
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-header-install-dir
|
|
(lambda _
|
|
;; As of the writing of this package, CMake and GNU build systems
|
|
;; install the header to two different location. This patch makes
|
|
;; the CMake build system's choice of header directory compatible
|
|
;; with the GNU build system's choice and with what avogadrolibs
|
|
;; expects.
|
|
;; See https://github.com/spglib/spglib/issues/75 and the relevant
|
|
;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
|
|
(substitute* "CMakeLists.txt"
|
|
(("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
|
|
(string-append include-dir "/spglib")))
|
|
#t)))))
|
|
(home-page "https://spglib.github.io/spglib/index.html")
|
|
(synopsis "Library for crystal symmetry search")
|
|
(description "Spglib is a library for finding and handling crystal
|
|
symmetries written in C. Spglib can be used to:
|
|
|
|
@enumerate
|
|
@item Find symmetry operations
|
|
@item Identify space-group type
|
|
@item Wyckoff position assignment
|
|
@item Refine crystal structure
|
|
@item Find a primitive cell
|
|
@item Search irreducible k-points
|
|
@end enumerate")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pymol
|
|
(package
|
|
(name "python-pymol")
|
|
(version "2.5.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/schrodinger/pymol-open-source")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:configure-flags
|
|
(list "--glut" "--testing")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'make-reproducible
|
|
(lambda _
|
|
(substitute* "create_shadertext.py"
|
|
(("time\\.time\\(\\)") "0"))))
|
|
(add-after 'unpack 'add-include-directories
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "CPLUS_INCLUDE_PATH"
|
|
(string-append (assoc-ref inputs "freetype")
|
|
"/include/freetype2:"
|
|
(assoc-ref inputs "libxml2")
|
|
"/include/libxml2:"
|
|
(getenv "CPLUS_INCLUDE_PATH")))))
|
|
;; The setup.py script does not support one of the Python build
|
|
;; system's default flags, "--single-version-externally-managed".
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(invoke "python" "setup.py" "install"
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
"--root=/"))))))
|
|
(inputs
|
|
(list freetype
|
|
libpng
|
|
freeglut
|
|
glew
|
|
libxml2
|
|
mmtf-cpp
|
|
msgpack
|
|
python-pyqt
|
|
glm
|
|
netcdf))
|
|
(native-inputs
|
|
(list catch-framework2 python-setuptools))
|
|
(home-page "https://pymol.org")
|
|
(synopsis "Molecular visualization system")
|
|
(description "PyMOL is a capable molecular viewer and renderer. It can be
|
|
used to prepare publication-quality figures, to share interactive results with
|
|
your colleagues, or to generate pre-rendered animations.")
|
|
(license license:bsd-3)))
|