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#!/usr/bin/env bash
# Simple command to run tests using installed bcbio_nextgen python/nose
# Can pass an optional argument with the type of tests to run
# ./run_tests.sh rnaseq
# ./run_tests.sh speed=1
# ./run_tests.sh devel
# ./run_tests.sh docker
# ./run_tests.sh docker_ipython
# Portable resolution of symlinks http://stackoverflow.com/a/24572274/252589
# readlink -f does not work on Macs
readlinkf(){ perl -MCwd -e 'print Cwd::abs_path shift' $1;}
MARK=${1:-speed1}
if [ -n "$1" ]; then
# Remaining args are passed unmodified to the test runner.
shift
fi
if [[ ${MARK} == docker* && "`which bcbio_vm.py`" != "" ]]; then
BCBIO_DIR=$(dirname "$(readlinkf `which bcbio_vm.py`)")
else
BCBIO_DIR=$(dirname "$(readlinkf `which bcbio_nextgen.py`)")
fi
unset PYTHONHOME
unset PYTHONPATH
export PYTHONNOUSERSITE=1
# Ensure version.py exists in raw cloned bcbio directory
if [ -d "../bcbio/pipeline" ]; then
[ -f ../bcbio/pipeline/version.py ] || touch ../bcbio/pipeline/version.py
fi
py.test-3 -p no:cacheprovider -p no:stepwise -v -s -m ${MARK} "$@"
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