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{ lib, stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }:
stdenv.mkDerivation rec {
pname = "cytoscape";
version = "3.10.1";
src = fetchurl {
url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz";
sha256 = "sha256-fqxAsnpMYCYj0hW2oxu/NH4PqesRlWPs5eDSeSjy1aU=";
};
patches = [
# By default, gen_vmoptions.sh tries to store custom options in $out/share
# at run time. This patch makes sure $HOME is used instead.
(substituteAll {
src = ./gen_vmoptions_to_homedir.patch;
inherit coreutils;
})
];
nativeBuildInputs = [ makeWrapper ];
buildInputs = [ jre ];
installPhase = ''
mkdir -pv $out/{share,bin}
cp -Rv * $out/share/
ln -s $out/share/cytoscape.sh $out/bin/cytoscape
wrapProgram $out/share/cytoscape.sh \
--set JAVA_HOME "${jre}" \
--set JAVA "${jre}/bin/java"
chmod +x $out/bin/cytoscape
'';
meta = {
homepage = "http://www.cytoscape.org";
description = "A general platform for complex network analysis and visualization";
mainProgram = "cytoscape";
license = lib.licenses.lgpl21;
maintainers = [lib.maintainers.mimame];
platforms = lib.platforms.unix;
};
}
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