knowengdev/simplified_inpherno_pipeline repository overview

⁠Simplified InPheRNo Pipeline

This is the Knowledge Engine for Genomics (KnowEnG), an NIH BD2K Center of Excellence, Simplified InPheRNo Pipeline.

Simplified InPheRNo Pipeline on Git Hub⁠

⁠How to run this pipeline with our example Data

Install Docker⁠

1. Pull and start the container connected to your local results directory. docker run -v local_results_dir:/home/test/run_dir -it knowengdev/simplified_inpherno_pipeline:08_07_2018

2. In the container now, at the command prompt switch to the test directory. cd test

3. Set up the environment. make env_setup

4. Run the pipeline with the template yaml file. make run_InPheRNo_simplified

5. To exit and stop the container (when processing is complete). exit

6. Results will be in the directory mounted with the docker run command (in step 1). /local_results_dir/