Merge pull request #231516 from benwbooth/jbrowse

jbrowse: init at 2.5.0

pkgs/applications/science/biology/jbrowse/default.nix

@@ -0,0 +1,39 @@
+{ lib, fetchurl, appimageTools, wrapGAppsHook }:
+
+let
+  pname = "jbrowse";
+  version = "2.5.0";
+
+  src = fetchurl {
+    url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage";
+    sha256 = "sha256-YLsyA+RVoFvjE4MfAtglJYdUgic487SxwdUhvolzBPc=";
+  };
+
+  appimageContents = appimageTools.extractType2 {
+    inherit pname version src;
+  };
+
+in
+appimageTools.wrapType2 {
+  inherit pname version src;
+  unshareIpc = false;
+
+  extraInstallCommands = ''
+    mkdir -p $out/bin
+    mv $out/bin/jbrowse-${version} $out/bin/jbrowse-desktop
+
+    install -m 444 -D ${appimageContents}/jbrowse-desktop.desktop $out/share/applications/jbrowse-desktop.desktop
+    install -m 444 -D ${appimageContents}/jbrowse-desktop.png \
+       $out/share/icons/hicolor/512x512/apps/jbrowse-desktop.png
+    substituteInPlace $out/share/applications/jbrowse-desktop.desktop \
+      --replace 'Exec=AppRun --no-sandbox' 'Exec=jbrowse-desktop'
+  '';
+
+  meta = with lib; {
+    description = "The next-generation genome browser";
+    homepage = "https://jbrowse.org/jb2/";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ benwbooth ];
+    platforms = [ "x86_64-linux" ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -9505,6 +9505,8 @@ with pkgs;
 
   jbofihe = callPackage ../tools/text/jbofihe { };
 
+  jbrowse = callPackage ../applications/science/biology/jbrowse { };
+
   jumanpp = callPackage ../tools/text/jumanpp { };
 
   jump = callPackage ../tools/system/jump { };