diff options
Diffstat (limited to 'pkgs/applications/science/misc')
4 files changed, 36 insertions, 8 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 $vm_options_path + fi + + # Determine amount of physical memory present: diff --git a/pkgs/applications/science/misc/foldingathome/control.nix b/pkgs/applications/science/misc/foldingathome/control.nix index 72217689ff18..91c3b8c779cd 100644 --- a/pkgs/applications/science/misc/foldingathome/control.nix +++ b/pkgs/applications/science/misc/foldingathome/control.nix @@ -8,7 +8,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; python = python2.withPackages ( @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb"; - sha256 = "1fh7ybbp3qlqzh18c4gva3aaymv7d31mqchrv235a1axldha1s9s"; + sha256 = "0qfvhwc29cgqkwf2bkhq4gr2d1c4jgccfs58916ss03n4rwz9gng"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index a35df650300b..cdeed6536efa 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -11,7 +11,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; in stdenv.mkDerivation rec { inherit version; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb"; - sha256 = "04wr86g11wpmsczzwzak4gvalcihb47rn3zp6qriawhxyac9nf93"; + sha256 = "09yfvk16j1iwx8h1xg678ks3bc8760gfdn7n32j8r893kd32cwyk"; }; nativeBuildInputs = [ |