cgat-tests

Configuration files for CI

Running cgat-test

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 git@github.com: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