Merge pull request #231516 from benwbooth/jbrowse

{ 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" ];

  };

}

  jbofihe = callPackage ../tools/text/jbofihe { };

  jbrowse = callPackage ../applications/science/biology/jbrowse { };

  jumanpp = callPackage ../tools/text/jumanpp { };

  jump = callPackage ../tools/system/jump { };