Merge pull request #86910 from lsix/cytoscape-3.8.0
cytoscape: 3.7.2 -> 3.8.0
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commit
b7c5508bfc
@ -1,14 +1,23 @@
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{ stdenv, fetchurl, jre, makeWrapper }:
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{ stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }:
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stdenv.mkDerivation rec {
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pname = "cytoscape";
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version = "3.7.2";
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version = "3.8.0";
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src = fetchurl {
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url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-${version}.tar.gz";
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sha256 = "125vgr8vqbmy2nsm1yl0h0q8p49lxxqfw5cmxzbx1caklcn4rryc";
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url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz";
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sha256 = "0kksx12m83cjprdygmcc286990byf25yqfx5s7c07cizc21aavyg";
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};
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patches = [
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# By default, gen_vmoptions.sh tries to store custom options in $out/share
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# at run time. This patch makes sure $HOME is used instead.
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(substituteAll {
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src = ./gen_vmoptions_to_homedir.patch;
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inherit coreutils;
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})
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];
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buildInputs = [jre makeWrapper];
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installPhase = ''
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@ -0,0 +1,19 @@
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diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh
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--- a/gen_vmoptions.sh 2020-03-30 21:57:47.000000000 +0100
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+++ b/gen_vmoptions.sh 2020-05-05 09:49:57.974989824 +0100
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@@ -1,13 +1,10 @@
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#!/bin/sh
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# Generates the Cytoscape.vmoptions file
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-script_path="$(dirname -- $0)"
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-
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-#vm_options_path="$HOME/.cytoscape"
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-vm_options_path=$script_path
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+vm_options_path="$HOME/.cytoscape"
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if [ ! -e $vm_options_path ]; then
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- /bin/mkdir $vm_options_path
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+ @coreutils@/bin/mkdir $vm_options_path
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fi
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# Determine amount of physical memory present:
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@ -25125,7 +25125,9 @@ in
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inherit (pkgs.gnome2) gtkglext;
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};
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cytoscape = callPackage ../applications/science/misc/cytoscape { };
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cytoscape = callPackage ../applications/science/misc/cytoscape {
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jre = openjdk11;
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};
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fityk = callPackage ../applications/science/misc/fityk { };
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