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Merge pull request #37855 from Mounium/chem3

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jmol init, pymol -> 2.1.0 and tidied up all-packages.nix
This commit is contained in:
Matthew Justin Bauer 2018-05-01 11:01:21 -05:00 committed by GitHub
commit 63666bf1d5
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 40 additions and 29 deletions
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27
pkgs/applications/science/chemistry/jmol/default.nix
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@ -1,9 +1,20 @@
{ stdenv
, fetchurl
, unzip
, makeDesktopItem
, jre
}:
let
desktopItem = makeDesktopItem {
name = "jmol";
exec = "jmol";
desktopName = "JMol";
genericName = "Molecular Modeler";
mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
categories = "Graphics;Education;Science;Chemistry;";
};
in
stdenv.mkDerivation rec {
version = "${baseVersion}.${patchVersion}";
baseVersion = "14.29";
@ -16,19 +27,18 @@ stdenv.mkDerivation rec {
sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
};
buildInputs = [
jre
];
patchPhase = ''
sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
'';
installPhase = ''
mkdir -p "$out/share/jmol"
mkdir -p "$out/bin"
mkdir -p "$out/share/jmol" "$out/bin"
${unzip}/bin/unzip jsmol.zip -d "$out/share/"
sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh
cp *.jar jmol.sh "$out/share/jmol"
ln -s $out/share/jmol/jmol.sh "$out/bin/jmol"
cp -r ${desktopItem}/share/applications $out/share
cp jmol $out/bin
'';
enableParallelBuilding = true;
@ -38,7 +48,6 @@ stdenv.mkDerivation rec {
homepage = https://sourceforge.net/projects/jmol;
license = licenses.lgpl2;
platforms = platforms.all;
maintainers = with maintainers; [ timokau ];
maintainers = with maintainers; [ timokau mounium ];
};
}

12
pkgs/applications/science/chemistry/pymol/default.nix
View File

@ -1,14 +1,14 @@
{ stdenv, fetchurl, makeDesktopItem
, python3, python3Packages
, glew, freeglut, libpng, libxml2, tk, freetype }:
, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }:
with stdenv.lib;
let
pname = "pymol";
ver_maj = "1.8";
ver_min = "4";
ver_maj = "2";
ver_min = "1";
version = "${ver_maj}.${ver_min}.0";
description = "A Python-enhanced molecular graphics tool";
@ -16,7 +16,7 @@ let
name = "${pname}";
exec = "${pname}";
desktopName = "PyMol Molecular Graphics System";
genericName = "Molecular Modeller";
genericName = "Molecular Modeler";
comment = description;
mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
categories = "Graphics;Education;Science;Chemistry;";
@ -26,10 +26,10 @@ python3Packages.buildPythonApplication {
name = "pymol-${version}";
src = fetchurl {
url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2";
sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n";
sha256 = "1qpacd5w4r9a0nm5iqmkd92ym3ai00dp7v61cwd6jgakk6wfps3s";
};
buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ];
buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype libmsgpack ];
NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
installPhase = ''

30
pkgs/top-level/all-packages.nix
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@ -2780,8 +2780,6 @@ with pkgs;
gvolicon = callPackage ../tools/audio/gvolicon {};
gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
gzip = callPackage ../tools/compression/gzip { };
gzrt = callPackage ../tools/compression/gzrt { };
@ -3124,8 +3122,6 @@ with pkgs;
jmespath = callPackage ../development/tools/jmespath { };
jmol = callPackage ../applications/science/chemistry/jmol { };
jmtpfs = callPackage ../tools/filesystems/jmtpfs { };
jnettop = callPackage ../tools/networking/jnettop { };
@ -3754,8 +3750,6 @@ with pkgs;
modsecurity_standalone = callPackage ../tools/security/modsecurity { };
molden = callPackage ../applications/science/chemistry/molden { };
molly-guard = callPackage ../os-specific/linux/molly-guard { };
moneyplex = callPackage ../applications/office/moneyplex { };
@ -7167,8 +7161,6 @@ with pkgs;
ocropus = callPackage ../applications/misc/ocropus { };
octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
inherit (callPackages ../development/interpreters/perl {}) perl perl522 perl524 perl526;
pachyderm = callPackage ../applications/networking/cluster/pachyderm { };
@ -14859,10 +14851,6 @@ with pkgs;
avidemux = libsForQt5.callPackage ../applications/video/avidemux { };
avogadro = callPackage ../applications/science/chemistry/avogadro {
eigen = eigen2;
};
avrdudess = callPackage ../applications/misc/avrdudess { };
avxsynth = callPackage ../applications/video/avxsynth {
@ -17419,8 +17407,6 @@ with pkgs;
puremapping = callPackage ../applications/audio/pd-plugins/puremapping { };
pymol = callPackage ../applications/science/chemistry/pymol { };
pybitmessage = callPackage ../applications/networking/instant-messengers/pybitmessage { };
pythonmagick = callPackage ../applications/graphics/PythonMagick { };
@ -19751,6 +19737,22 @@ with pkgs;
### SCIENCE
### SCIENCE/CHEMISTY
avogadro = callPackage ../applications/science/chemistry/avogadro {
eigen = eigen2;
};
gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
jmol = callPackage ../applications/science/chemistry/jmol { };
molden = callPackage ../applications/science/chemistry/molden { };
octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
pymol = callPackage ../applications/science/chemistry/pymol { };
### SCIENCE/GEOMETRY
drgeo = callPackage ../applications/science/geometry/drgeo {