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75 lines
1.8 KiB
Nix
75 lines
1.8 KiB
Nix
{
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lib,
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stdenv,
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fetchurl,
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python3Packages,
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zlib,
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bash,
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}:
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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 = "5.3.0";
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format = "setuptools";
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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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hash = "sha256-rJ26A++dClHXqeLFaCYQTnjzQPYmOjrTk2SEQt68dOw=";
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};
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pythonPath = with pythonPackages; [
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simplejson
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joblib
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setuptools
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distutils
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matplotlib
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];
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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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${python.pythonOnBuildForHost.interpreter} setup.py install \
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--install-lib=$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 $old_rpath:${lib.getLib stdenv.cc.cc}/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 = {
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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 lib.sourceTypes; [
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fromSource
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binaryNativeCode # source bundles binary dependencies
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];
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license = lib.licenses.gpl2;
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maintainers = [ lib.maintainers.bzizou ];
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platforms = lib.platforms.all;
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};
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}
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