50 lines
1.9 KiB
ReStructuredText
50 lines
1.9 KiB
ReStructuredText
.. _analysis-workflow-example:
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Analysis Workflow Example
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==========================
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This is a quick guide for creating and running a simple pipeline to analysis an example dataset with 2 participants.
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#. Install RAPIDS. See :ref:`Installation Section <install-page>`.
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#. Configure your database credentials (see the example below or step 1 of :ref:`Usage Section <db-configuration>` for more information).
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- Create an ``.env`` file at the root of RAPIDS folder
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- Your MySQL user must have write permissions because we will restore our example database
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- Name your credentials group ``MY_GROUP``.
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- If you are trying to connect to a local MySQL server from our docker container set your host according to this link_.
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- You can name your database any way you want, for example ``rapids_example``
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.. code-block:: bash
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[MY_GROUP]
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user=rapids
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password=rapids
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host=127.0.0.1
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port=3306
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database=rapids_example
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#. Make sure your conda environment is active (the environment is already active in our docker container). See step 6 of :ref:`install-page`.
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#. If you installed RAPIDS from GitHub (did not use docker) you need to download the `example db backup <https://osf.io/skqfv/files/>`_ and save it to ``data/external/rapids_example.sql``.
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#. Run the following command to restore database from ``rapids_example.sql`` file::
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snakemake -j1 restore_sql_file
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#. Create example participants files with the following command::
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snakemake -j1 create_example_participant_files
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#. Run the following command to analysis the example dataset.
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- Execute over a single core::
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snakemake -j1 --profile example_profile
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- Execute over multiple cores (here, we use 8 cores)::
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snakemake -j8 --profile example_profile
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.. _link: https://stackoverflow.com/questions/24319662/from-inside-of-a-docker-container-how-do-i-connect-to-the-localhost-of-the-mach
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