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{ gevent
, buildPythonPackage
, fetchFromGitHub
, hostname
, pytest
, python
, stdenv
}:
buildPythonPackage rec {
pname = "ruffus";
version = "2.8.1";
src = fetchFromGitHub {
owner = "cgat-developers";
repo = pname;
rev = "v${version}";
sha256 = "1gyabqafq4s2sy0prh3k1m8859shzjmfxr7fimx10liflvki96a9";
};
propagatedBuildInputs = [ gevent ];
postPatch = ''
sed -i -e 's|/bin/bash|${stdenv.shell}|' ruffus/test/Makefile
sed -i -e 's|\tpytest|\t${pytest}/bin/pytest|' ruffus/test/Makefile
sed -i -e 's|\tpython|\t${python.interpreter}|' ruffus/test/Makefile
sed -i -e 's|/usr/bin/env bash|${stdenv.shell}|' ruffus/test/run_all_unit_tests.cmd
sed -i -e 's|python3|${python.interpreter}|' ruffus/test/run_all_unit_tests3.cmd
sed -i -e 's|python %s|${python.interpreter} %s|' ruffus/test/test_drmaa_wrapper_run_job_locally.py
'';
makefile = "ruffus/test/Makefile";
checkInputs = [
gevent
hostname
pytest
];
checkPhase = ''
export HOME=$TMPDIR
cd ruffus/test
make all PYTEST_OPTIONS="-q --disable-warnings"
'';
meta = with stdenv.lib; {
description = "Light-weight Python Computational Pipeline Management";
homepage = http://www.ruffus.org.uk;
license = licenses.mit;
maintainers = [ maintainers.kiwi ];
};
}
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