vep: init at 110 (#283317)

# Instructions:http://www.ensembl.org/info/docs/api/api_installation.html,

# Do not use https://github.com/Ensembl/ensembl-vep/archive/release/${version}.zip

# We cannot use INSTALL.pl but it’s not that bad:install the dependencies and copies the .pm files should be ok

{

  lib,

  htslib,

  perlPackages,

  stdenv,

  fetchFromGitHub,

  perl,

  makeWrapper,

}:

let

  version = "110";

  customInstallPhase = ''

    mkdir -p $out/${perl.libPrefix}/${perl.version}/

    tests=$(find modules/ -mindepth 1 -maxdepth 1 -type d | grep -v t)

    cp -r $tests $out/${perl.libPrefix}/${perl.version}/

  '';

  ensemblGit =

    name: sha256:

    # Copy modules directly

    stdenv.mkDerivation {

      inherit name version;

      src = fetchFromGitHub {

        inherit sha256 version;

        owner = "Ensembl";

        repo = name;

        rev = "release/${version}";

      };

      installPhase = ''

        runHook preInstall

        ${customInstallPhase}

        runHook postInstall'';

    };

  vepPlugins = fetchFromGitHub {

    owner = "Ensembl";

    repo = "VEP_plugins";

    rev = "8f271c4848338dc7d504881ff71fdf2892c3d096";

    sha256 = "sha256-LbaXwLFDP3m1QhRHwO9uh36BEFHE2NzL4xdxTb7/S5Q=";

  };

  # Install ensembl-xs, faster run using re-implementation in C of some of the Perl subroutines

  ensembl-xs = perlPackages.buildPerlPackage rec {

    pname = "ensembl-xs";

    version = "2.3.2";

    src = fetchFromGitHub {

      inherit version;

      owner = "Ensembl";

      repo = "ensembl-xs";

      rev = version;

      sha256 = "1qqnski532f4bz32wxbqd9w1sz40rjh81ipp9p02k3rlaf1gp1fa";

    };

    # PREFIX is important

    configurePhase = ''

      perl Makefile.PL PREFIX=$out INSTALLDIRS=site

    '';

    # Test do not work -- wrong include path

    doCheck = false;

  };

  # it contains compiled versions of certain key subroutines used in VEP

  ensembl = ensemblGit "ensembl" "sha256-ZhI4VNxIY+53RX2uYRNlFeo/ydAmlwGx00WDXaxv6h4=";

  ensembl-io = ensemblGit "ensembl-io" "sha256-r3RvN5U2kcyghoKM0XuiBRe54t1U4FaZ0QEeYIFiG0w=";

  ensembl-variation = ensemblGit "ensembl-variation" "sha256-UjrLHF9EqI+Mp+SZR4sLNZUCGiA/UYhoFWtpwiKF8tM=";

  ensembl-funcgen = ensemblGit "ensembl-funcgen" "sha256-a9hxLBoXJsF5JWuRdpyOac1u033M8ivEjEQecuncghs=";

in

perlPackages.buildPerlModule rec {

  inherit version;

  pname = "vep";

  buildInputs =

    (with perlPackages; [

      ArchiveZip

      BioBigFile

      BioDBHTS

      BioExtAlign

      BioPerl

      DBI

      DBDmysql

      LWP

      JSON

    ])

    ++ [

      ensembl-xs

      ensembl

      ensembl-funcgen

      ensembl-io

      ensembl-variation

    ];

  propagatedBuildInputs = [ htslib ];

  src = fetchFromGitHub {

    owner = "Ensembl";

    repo = "ensembl-${pname}";

    rev = "release/${version}";

    sha256 = "sha256-6lRdWV2ispl+mpBhkZez/d9PxOw1fkNUWeG8mUIqBJc=";

  };

  nativeBuildInputs = [ makeWrapper ];

  dontBuild = true;

  doCheck = false;

  outputs = [ "out" ];

  installPhase = ''

    runHook preInstall

    mkdir -p $out/bin

    install -D -m755 filter_vep vep $out/bin/

    wrapProgram $out/bin/vep \

      --prefix PERL5LIB : $out/${perl.libPrefix}/${perl.version}/ \

      --add-flags "--dir_plugins ${vepPlugins}"

    wrapProgram $out/bin/filter_vep \

      --prefix PERL5LIB : $out/${perl.libPrefix}/${perl.version}/

    ${customInstallPhase}

    runHook postInstall

  '';

  meta = {

    homepage = "https://www.ensembl.org/info/docs/tools/vep/index.html";

    description = "Annotate genetics variants based on genes, transcripts, and protein sequence, as well as regulatory regions";

    license = lib.licenses.asl20;

    mainProgram = "vep";

    maintainers = with lib.maintainers; [ apraga ];

    platforms = lib.platforms.unix;

  };

}