rapids/docs/usage/example.rst

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.. _analysis-workflow-example
Analysis Workflow Example
==========================
This is a quick guide for creating and running a simple pipeline to analysis an example dataset with 2 participants.
#. Install RAPIDS. See :ref:`Installation Section <install-page>`.
#. Make sure your database connection credentials in ``.env`` have write permission and set the correct ``MY_GROUP`` parameter in ``example_profile/example_config.yaml`` file. See step 1 of :ref:`Usage Section <db-configuration>`.
#. Make sure your Conda (python) environment is active. See step 6 of :ref:`install-page`.
#. Run the following command to restore database from ``rapids_example.sql`` file::
sankemake -j1 restore_sql_file
#. Create example participants files with the following command::
snakemake -j1 create_example_participant_files
#. Run the following command to analysis the example dataset.
- Execute over a single core::
snakemake -j1 --profile example_profile
- Execute over multiple cores (here, we use 8 cores)::
snakemake -j8 --profile example_profile