Gadget PD Pipeline
A pipeline for differentiating and categorizing patients of Parkinsons and Essential Tremor using a mixture of genetic and motion tracking techniques.
Using this pipeline
This pipeline is built using metapipe and a variety of other tools. Install the dependencies as follows:
$ pip install -r requirements.txt
Once all the dependencies are installed, the next step is to execute the pipeline. If you wish to run it locally, then use the following command:
$ sh run_me.sh <sample_id> <API_USERNAME> <API_PASSWORD>
To run this pipeline on an external system, like a cluster, you'll need to edit the pipeline.mp file and fill in your api username, password, and sample id. When that is done, run your pipeline using these commands:
$ metapipe -j pbs -o pipeline.sh pipeline.mp
$ qsub pipeline.sh
Project Organization
This project relies on a few external projects and a variety of shell scripts.
The shell scripts can be found in the bin/
directory, and the related
packages are in the requirements.txt.
The overall structure of the pipeline can be found in the pipeline.mp file. This file contains the metapipe-format pipeline design.