diff options
| author | Lancelot SIX <lsix@lancelotsix.com> | 2020-05-05 09:52:27 +0100 |
|---|---|---|
| committer | Lancelot SIX <lsix@lancelotsix.com> | 2020-05-05 09:52:27 +0100 |
| commit | b9d13090a86f735dfe9fbd5da357302b1896b6f4 (patch) | |
| tree | 8af2c0e1e283dea5c4e605338ebb6dcaaa1bac94 | |
| parent | knot-dns: 2.9.3 -> 2.9.4 (diff) | |
| download | nixpkgs-origin/cytoscape-3.8.0.tar.gz | |
cytoscape: 3.7.2 -> 3.8.0origin/cytoscape-3.8.0
See https://cytoscape.org/release_notes_3_8_0.html for release
information
| -rw-r--r-- | pkgs/applications/science/misc/cytoscape/default.nix | 17 | ||||
| -rw-r--r-- | pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch | 19 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 4 |
3 files changed, 35 insertions, 5 deletions
diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index b4e4adbfa6f2..0db007f543f3 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 $HOME is used instead. + (substituteAll { + src = ./gen_vmoptions_to_homedir.patch; + inherit coreutils; + }) + ]; + buildInputs = [jre makeWrapper]; installPhase = '' diff --git a/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch new file mode 100644 index 000000000000..e31681e8541f --- /dev/null +++ b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch @@ -0,0 +1,19 @@ +diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh +--- a/gen_vmoptions.sh 2020-03-30 21:57:47.000000000 +0100 ++++ b/gen_vmoptions.sh 2020-05-05 09:49:57.974989824 +0100 +@@ -1,13 +1,10 @@ + #!/bin/sh + # Generates the Cytoscape.vmoptions file + +-script_path="$(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 95517f754119..eab964e52621 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 { }; |