From b9d13090a86f735dfe9fbd5da357302b1896b6f4 Mon Sep 17 00:00:00 2001
From: Lancelot SIX <lsix@lancelotsix.com>
Date: Tue, 5 May 2020 09:52:27 +0100
Subject: [PATCH] cytoscape: 3.7.2 -> 3.8.0

See https://cytoscape.org/release_notes_3_8_0.html for release
information
---
 .../science/misc/cytoscape/default.nix        | 17 +++++++++++++----
 .../cytoscape/gen_vmoptions_to_homedir.patch  | 19 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  4 +++-
 3 files changed, 35 insertions(+), 5 deletions(-)
 create mode 100644 pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch

diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix
index b4e4adbfa6f..0db007f543f 100644
--- a/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/pkgs/applications/science/misc/cytoscape/default.nix
@@ -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 = ''
diff --git a/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch
new file mode 100644
index 00000000000..e31681e8541
--- /dev/null
+++ b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch
@@ -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:
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 95517f75411..eab964e5262 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -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 { };