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