Analysis Workflow Example

This is a quick guide for creating and running a simple pipeline to analysis an example dataset with 2 participants.

1. Install RAPIDS. See Installation Section.

2. Configure your database credentials (see the example below or step 1 of Usage Section for more information).

   • Create an .env file at the root of RAPIDS folder
   • Your MySQL user must have write permissions because we will restore our example database
   • Name your credentials group MY_GROUP.
   • If you are trying to connect to a local MySQL server from our docker container set your host according to this link.
   • You can name your database any way you want, for example rapids_example

   [MY_GROUP]
   user=rapids
   password=rapids
   host=127.0.0.1
   port=3306
   database=rapids_example
   

3. Make sure your conda environment is active (the environment is already active in our docker container). See step 6 of Installation.

4. If you installed RAPIDS from GitHub (did not use docker) you need to download the example db backup and save it to data/external/rapids_example.sql.

5. Run the following command to restore database from rapids_example.sql file:

   snakemake -j1 restore_sql_file
   

6. Create example participants files with the following command:

   snakemake -j1 create_example_participant_files
   

7. 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