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|
{ lib, stdenv
, libpng
, libuuid
, zlib
, bzip2
, xz
, openssl
, curl
, libmysqlclient
, bash
, fetchFromGitHub
, which
}:
stdenv.mkDerivation rec {
pname = "kent";
version = "467";
src = fetchFromGitHub {
owner = "ucscGenomeBrowser";
repo = pname;
rev = "v${version}_base";
hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE=";
};
buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];
postPatch = ''
substituteInPlace ./src/checkUmask.sh \
--replace "/bin/bash" "${bash}/bin/bash"
substituteInPlace ./src/hg/sqlEnvTest.sh \
--replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"
'';
buildPhase = ''
runHook preBuild
export MACHTYPE=$(uname -m)
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/x86_64
cd ./src
chmod +x ./checkUmask.sh
./checkUmask.sh
make libs
cd jkOwnLib
make
cp ../lib/x86_64/jkOwnLib.a $HOME/lib
cp ../lib/x86_64/jkweb.a $HOME/lib
cp -r ../inc $HOME/
cd ../utils
make
runHook postBuild
'';
installPhase = ''
runHook preInstall
mkdir -p $out/bin $out/lib $out/inc
cp $HOME/lib/jkOwnLib.a $out/lib
cp $HOME/lib/jkweb.a $out/lib
cp $HOME/bin/x86_64/* $out/bin
cp -r $HOME/inc/* $out/inc/
runHook postInstall
'';
meta = with lib; {
description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities";
homepage = "http://genome.ucsc.edu";
changelog = "https://github.com/ucscGenomeBrowser/kent/releases/tag/v${version}_base";
license = licenses.unfree;
maintainers = with maintainers; [ scalavision ];
platforms = platforms.linux;
};
}
|
