Unverified Commit 45e261e7 authored by Peder Bergebakken Sundt's avatar Peder Bergebakken Sundt Committed by GitHub
Browse files

kent: 468 -> 486 (#438937)

parents 3576a325 bf210e08

pkgs/by-name/ke/kent/package.nix

+19 −9
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  writableTmpDirAsHomeHook,

  libpng,

  libuuid,

  zlib,
@@ -12,18 +13,23 @@ 
  bash,

  fetchFromGitHub,

  which,

  writeShellScript,

  jq,

  nix-update,

}:

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "kent";

  version = "468";

  version = "486";



  src = fetchFromGitHub {

    owner = "ucscGenomeBrowser";

    repo = "kent";

    rev = "v${version}_base";

    hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA=";

    tag = "v${finalAttrs.version}_base";

    hash = "sha256-NffQ04+5rMtG/VI7YFK4Ff39DDhdh9Wlc0i1iVbg8Js=";

  };



  nativeBuildInputs = [ writableTmpDirAsHomeHook ];



  buildInputs = [

    libpng

    libuuid
@@ -37,10 +43,10 @@ stdenv.mkDerivation rec { 


  postPatch = ''

    substituteInPlace ./src/checkUmask.sh \

      --replace "/bin/bash" "${bash}/bin/bash"

      --replace-fail "/bin/bash" "${bash}/bin/bash"



    substituteInPlace ./src/hg/sqlEnvTest.sh \

      --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"

      --replace-fail "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"

  '';



  buildPhase = ''
@@ -50,7 +56,6 @@ stdenv.mkDerivation rec { 
    export CFLAGS="-fPIC"

    export MYSQLINC=$(mysql_config --include | sed -e 's/^-I//g')

    export MYSQLLIBS=$(mysql_config --libs)

    export HOME=$TMPDIR

    export DESTBINDIR=$HOME/bin



    mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}
@@ -85,12 +90,17 @@ stdenv.mkDerivation rec { 
    runHook postInstall

  '';



  passthru.updateScript = writeShellScript "update-kent" ''

    latestVersion=$(curl ''${GITHUB_TOKEN:+-u ":$GITHUB_TOKEN"} --fail --silent https://api.github.com/repos/ucscGenomeBrowser/kent/releases/latest | ${lib.getExe jq} --raw-output .tag_name | grep -oP '(?<=v)\d+')

    ${lib.getExe nix-update} kent --version $latestVersion

  '';



  meta = {

    description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities";

    homepage = "http://genome.ucsc.edu";

    changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${version}_base";

    changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${finalAttrs.version}_base";

    license = lib.licenses.unfree;

    maintainers = with lib.maintainers; [ scalavision ];

    platforms = lib.platforms.linux;

  };

}
 
})