TorkamaniLab/gadget-pipeline

Name: gadget-pipeline

Owner: The Scripps Research Institute - Torkamani Lab

Description: An analysis pipeline used to classify ET vs. PD tremor based on wrist-mounted accelerometer data.

Created: 2016-03-23 20:49:18.0

Updated: 2016-03-24 00:00:27.0

Pushed: 2016-03-30 22:48:10.0

Homepage: null

Size: 13

Language: Shell

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README

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:

p 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:

 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:

tapipe -j pbs -o pipeline.sh pipeline.mp 
ub 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.