646b892680
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107 lines
2.5 KiB
Nix
107 lines
2.5 KiB
Nix
{
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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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bzip2,
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xz,
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openssl,
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curl,
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libmysqlclient,
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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 (finalAttrs: {
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pname = "kent";
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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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tag = "v${finalAttrs.version}_base";
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hash = "sha256-NffQ04+5rMtG/VI7YFK4Ff39DDhdh9Wlc0i1iVbg8Js=";
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};
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nativeBuildInputs = [ writableTmpDirAsHomeHook ];
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buildInputs = [
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libpng
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libuuid
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zlib
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bzip2
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xz
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openssl
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curl
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libmysqlclient
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];
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postPatch = ''
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substituteInPlace ./src/checkUmask.sh \
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--replace-fail "/bin/bash" "${bash}/bin/bash"
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substituteInPlace ./src/hg/sqlEnvTest.sh \
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--replace-fail "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"
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'';
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buildPhase = ''
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runHook preBuild
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export MACHTYPE=$(uname -m)
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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 DESTBINDIR=$HOME/bin
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mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}
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cd ./src
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chmod +x ./checkUmask.sh
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./checkUmask.sh
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make libs
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cd jkOwnLib
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make
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cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkOwnLib.a $HOME/lib
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cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkweb.a $HOME/lib
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cp -r ../inc $HOME/
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cd ../utils
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make
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runHook postBuild
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'';
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installPhase = ''
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runHook preInstall
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mkdir -p $out/bin $out/lib $out/inc
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cp $HOME/lib/jkOwnLib.a $out/lib
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cp $HOME/lib/jkweb.a $out/lib
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cp $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}/* $out/bin
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cp -r $HOME/inc/* $out/inc/
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runHook postInstall
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'';
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passthru.updateScript = writeShellScript "update-kent" ''
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latestVersion=$(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 $latestVersion
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'';
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meta = {
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description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities";
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homepage = "http://genome.ucsc.edu";
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changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${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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