Merge pull request #37855 from Mounium/chem3
jmol init, pymol -> 2.1.0 and tidied up all-packages.nix
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commit
63666bf1d5
@ -1,9 +1,20 @@
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{ stdenv
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, fetchurl
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, unzip
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, makeDesktopItem
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, jre
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}:
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let
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desktopItem = makeDesktopItem {
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name = "jmol";
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exec = "jmol";
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desktopName = "JMol";
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genericName = "Molecular Modeler";
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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;";
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categories = "Graphics;Education;Science;Chemistry;";
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};
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in
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stdenv.mkDerivation rec {
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version = "${baseVersion}.${patchVersion}";
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baseVersion = "14.29";
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@ -16,19 +27,18 @@ stdenv.mkDerivation rec {
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sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
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};
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buildInputs = [
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jre
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];
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patchPhase = ''
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sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
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'';
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installPhase = ''
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mkdir -p "$out/share/jmol"
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mkdir -p "$out/bin"
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mkdir -p "$out/share/jmol" "$out/bin"
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${unzip}/bin/unzip jsmol.zip -d "$out/share/"
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sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh
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cp *.jar jmol.sh "$out/share/jmol"
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ln -s $out/share/jmol/jmol.sh "$out/bin/jmol"
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cp -r ${desktopItem}/share/applications $out/share
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cp jmol $out/bin
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'';
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enableParallelBuilding = true;
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@ -38,7 +48,6 @@ stdenv.mkDerivation rec {
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homepage = https://sourceforge.net/projects/jmol;
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license = licenses.lgpl2;
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platforms = platforms.all;
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maintainers = with maintainers; [ timokau ];
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maintainers = with maintainers; [ timokau mounium ];
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};
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}
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@ -1,14 +1,14 @@
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{ stdenv, fetchurl, makeDesktopItem
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, python3, python3Packages
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, glew, freeglut, libpng, libxml2, tk, freetype }:
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, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }:
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with stdenv.lib;
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let
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pname = "pymol";
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ver_maj = "1.8";
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ver_min = "4";
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ver_maj = "2";
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ver_min = "1";
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version = "${ver_maj}.${ver_min}.0";
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description = "A Python-enhanced molecular graphics tool";
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@ -16,7 +16,7 @@ let
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name = "${pname}";
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exec = "${pname}";
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desktopName = "PyMol Molecular Graphics System";
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genericName = "Molecular Modeller";
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genericName = "Molecular Modeler";
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comment = description;
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mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
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categories = "Graphics;Education;Science;Chemistry;";
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@ -26,10 +26,10 @@ python3Packages.buildPythonApplication {
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name = "pymol-${version}";
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src = fetchurl {
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url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2";
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sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n";
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sha256 = "1qpacd5w4r9a0nm5iqmkd92ym3ai00dp7v61cwd6jgakk6wfps3s";
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};
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buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ];
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buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype libmsgpack ];
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NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
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installPhase = ''
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@ -2780,8 +2780,6 @@ with pkgs;
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gvolicon = callPackage ../tools/audio/gvolicon {};
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gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
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gzip = callPackage ../tools/compression/gzip { };
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gzrt = callPackage ../tools/compression/gzrt { };
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@ -3124,8 +3122,6 @@ with pkgs;
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jmespath = callPackage ../development/tools/jmespath { };
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jmol = callPackage ../applications/science/chemistry/jmol { };
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jmtpfs = callPackage ../tools/filesystems/jmtpfs { };
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jnettop = callPackage ../tools/networking/jnettop { };
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@ -3754,8 +3750,6 @@ with pkgs;
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modsecurity_standalone = callPackage ../tools/security/modsecurity { };
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molden = callPackage ../applications/science/chemistry/molden { };
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molly-guard = callPackage ../os-specific/linux/molly-guard { };
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moneyplex = callPackage ../applications/office/moneyplex { };
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@ -7167,8 +7161,6 @@ with pkgs;
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ocropus = callPackage ../applications/misc/ocropus { };
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octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
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inherit (callPackages ../development/interpreters/perl {}) perl perl522 perl524 perl526;
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pachyderm = callPackage ../applications/networking/cluster/pachyderm { };
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@ -14859,10 +14851,6 @@ with pkgs;
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avidemux = libsForQt5.callPackage ../applications/video/avidemux { };
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avogadro = callPackage ../applications/science/chemistry/avogadro {
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eigen = eigen2;
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};
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avrdudess = callPackage ../applications/misc/avrdudess { };
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avxsynth = callPackage ../applications/video/avxsynth {
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@ -17419,8 +17407,6 @@ with pkgs;
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puremapping = callPackage ../applications/audio/pd-plugins/puremapping { };
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pymol = callPackage ../applications/science/chemistry/pymol { };
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pybitmessage = callPackage ../applications/networking/instant-messengers/pybitmessage { };
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pythonmagick = callPackage ../applications/graphics/PythonMagick { };
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@ -19751,6 +19737,22 @@ with pkgs;
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### SCIENCE
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### SCIENCE/CHEMISTY
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avogadro = callPackage ../applications/science/chemistry/avogadro {
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eigen = eigen2;
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};
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gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
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jmol = callPackage ../applications/science/chemistry/jmol { };
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molden = callPackage ../applications/science/chemistry/molden { };
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octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
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pymol = callPackage ../applications/science/chemistry/pymol { };
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### SCIENCE/GEOMETRY
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drgeo = callPackage ../applications/science/geometry/drgeo {
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