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import os
import pytest
import sys
from pbcore.io.dataset.utils import which
def _check_constools():
return which('pbindex') and which('samtools') and which('pbmerge')
def _internal_data():
return os.path.exists("/pbi/dept/secondary/siv/testdata")
def pytest_runtest_setup(item):
for mark in item.iter_markers():
if mark.name == 'internal_data':
if not _internal_data():
pytest.skip(
"need access to '/pbi/dept/secondary/siv/testdata'")
elif mark.name == 'constools':
if not _check_constools():
pytest.skip("need 'pbindex'/'samtools'/'pbmerge'")
else:
raise LookupError("Unknown pytest mark: '{}'".format(mark.name))
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