Configuration files for CI
The tests are implemented in the script pipeline_testing.py, which is itself a ruffus pipeline. See its documentation to see how it works. To run the default CGAT pipeline tests, follow the following instructions::
# checkout configuration files into directory tests
git clone [email protected]:cgat-developers/cgat-tests.git
# enter tests directory
cd cgat-tests
# run pipeline_testing
python <path to code>/CGATPipelines/pipeline_testing.py make full -v 5 -p 10
# build report
python <path to code>/CGATPipelines/pipeline_testing.py make build_report -v 5 -p 10
This will run the default CGAT pipeline test suite and build a report. pipeline_testing.py performs the following actions:
- Download the test data and reference data from a tar-ball on http://www.cgat.org/downloads/public/cgatpipelines/pipeline_test_data.
- Unpack the data
- Run the tests
- Check the output of the tests against the reference data