cytoscape: 3.7.2 -> 3.8.0

See https://cytoscape.org/release_notes_3_8_0.html for release
information
This commit is contained in:
Lancelot SIX 2020-05-05 09:52:27 +01:00
parent 2147dd0648
commit b9d13090a8
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GPG key ID: 02E1542BA66FB047
3 changed files with 35 additions and 5 deletions

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@ -1,14 +1,23 @@
{ stdenv, fetchurl, jre, makeWrapper }:
{ stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }:
stdenv.mkDerivation rec {
pname = "cytoscape";
version = "3.7.2";
version = "3.8.0";
src = fetchurl {
url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-${version}.tar.gz";
sha256 = "125vgr8vqbmy2nsm1yl0h0q8p49lxxqfw5cmxzbx1caklcn4rryc";
url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz";
sha256 = "0kksx12m83cjprdygmcc286990byf25yqfx5s7c07cizc21aavyg";
};
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;
})
];
buildInputs = [jre makeWrapper];
installPhase = ''

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@ -0,0 +1,19 @@
diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh
--- a/gen_vmoptions.sh 2020-03-30 21:57:47.000000000 +0100
+++ b/gen_vmoptions.sh 2020-05-05 09:49:57.974989824 +0100
@@ -1,13 +1,10 @@
#!/bin/sh
# Generates the Cytoscape.vmoptions file
-script_path="$(dirname -- $0)"
-
-#vm_options_path="$HOME/.cytoscape"
-vm_options_path=$script_path
+vm_options_path="$HOME/.cytoscape"
if [ ! -e $vm_options_path ]; then
- /bin/mkdir $vm_options_path
+ @coreutils@/bin/mkdir $vm_options_path
fi
# Determine amount of physical memory present:

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@ -25004,7 +25004,9 @@ in
inherit (pkgs.gnome2) gtkglext;
};
cytoscape = callPackage ../applications/science/misc/cytoscape { };
cytoscape = callPackage ../applications/science/misc/cytoscape {
jre = openjdk11;
};
fityk = callPackage ../applications/science/misc/fityk { };