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{ lib, stdenv, fetchurl, python3Packages, zlib, bash }:
let
pythonPackages = python3Packages;
inherit (pythonPackages) python;
in
pythonPackages.buildPythonApplication rec {
pname = "quast";
version = "5.0.2";
src = fetchurl {
url = "https://github.com/ablab/quast/releases/download/${pname}_${version}/${pname}-${version}.tar.gz";
sha256 = "13ml8qywbb4cc7wf2x7z5mz1rjqg51ab8wkizwcg4f6c40zgif6d";
};
pythonPath = with pythonPackages; [ simplejson joblib setuptools matplotlib ];
buildInputs = [ zlib ] ++ pythonPath;
dontConfigure = true;
dontBuild = true;
installPhase = ''
substituteInPlace quast_libs/bedtools/Makefile \
--replace "/bin/bash" "${bash}/bin/bash"
mkdir -p "$out/${python.sitePackages}"
export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
${python.pythonForBuild.interpreter} setup.py install \
--install-lib=$out/${python.sitePackages} \
--prefix="$out"
'';
postFixup = ''
for file in $(find $out -type f -type f -perm /0111); do
old_rpath=$(patchelf --print-rpath $file) && \
patchelf --set-rpath $old_rpath:${stdenv.cc.cc.lib}/lib $file || true
done
# Link to the master program
ln -s $out/bin/quast.py $out/bin/quast
'';
dontPatchELF = true;
# Tests need to download data files, so manual run after packaging is needed
doCheck = false;
meta = with lib ; {
description = "Evaluates genome assemblies by computing various metrics";
homepage = "https://github.com/ablab/quast";
sourceProvenance = with sourceTypes; [
fromSource
binaryNativeCode # source bundles binary dependencies
];
license = licenses.gpl2;
maintainers = [ maintainers.bzizou ];
platforms = platforms.all;
};
}
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