commit 45e261e7bad6f6f7b8ad47e5ff3b7cdbeed1d4d0 · pyrox.dev/nixpkgs

+19 -9
pkgs/by-name/ke/kent/package.nix
···

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       {

     

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         lib,

     

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         stdenv,

     

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       +
         writableTmpDirAsHomeHook,

     

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         libpng,

     

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         libuuid,

     

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         zlib,

     
···

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         bash,

     

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         fetchFromGitHub,

     

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         which,

     

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       +
         writeShellScript,

     

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         jq,

     

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         nix-update,

     

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       }:

     

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       -
       stdenv.mkDerivation rec {

     

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       +
       stdenv.mkDerivation (finalAttrs: {

     

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         pname = "kent";

     

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       -
         version = "468";

     

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         version = "486";

     

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         src = fetchFromGitHub {

     

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           owner = "ucscGenomeBrowser";

     

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           repo = "kent";

     

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       -
           rev = "v${version}_base";

     

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

     

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

     

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

     

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         };

     

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       +
       

     

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         nativeBuildInputs = [ writableTmpDirAsHomeHook ];

     

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         buildInputs = [

     

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           libpng

     
···

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         postPatch = ''

     

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           substituteInPlace ./src/checkUmask.sh \

     

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

     

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

     

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           substituteInPlace ./src/hg/sqlEnvTest.sh \

     

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

     

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

     

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         '';

     

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         buildPhase = ''

     
···

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           export CFLAGS="-fPIC"

     

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

     

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           export MYSQLLIBS=$(mysql_config --libs)

     

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           export HOME=$TMPDIR

     

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           export DESTBINDIR=$HOME/bin

     

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           mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}

     
···

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           runHook postInstall

     

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         '';

     

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

     

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           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+')

     

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

     

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         '';

     

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         meta = {

     

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

     

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

     

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

     

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

     

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           license = lib.licenses.unfree;

     

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           maintainers = with lib.maintainers; [ scalavision ];

     

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           platforms = lib.platforms.linux;

     

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         };

     

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       -
       }

     

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       +
       })