ENCODE Hi-C uniform processing pipeline

Overview

The ENCODE pipeline for processing Hi-C data based on Juicer

Installation

1. Git clone this pipeline.

   $ git clone https://github.com/ENCODE-DCC/hic-pipeline

2. Install Caper, requires java >= 1.8 and python >= 3.6, Caper >= 0.8.2.1 is required to run the pipeline. Caper is a Python wrapper for Cromwell.

   $ pip install caper  # use pip3 if it doesn't work

3. Follow Caper's README carefully to configure it for your platform (local, cloud, cluster, etc.)

   IMPORTANT: Configure your Caper configuration file ~/.caper/default.conf correctly for your platform.

Usage

To verify your installation, you can run the following pipeline with a test data set by invoking the following command from the root of the cloned repository.

Note: this will incur some cost when running in cloud environments.

$ caper run hic.wdl -i tests/functional/json/test_hic.json

To run locally, you must first install docker. Then run the following command:

$ caper run hic.wdl -i tests/functional/json/test_hic.json --docker

For detailed usage, see usage

Inputs

See inputs

Outputs

See outputs

Contributing

We welcome comments, questions, suggestions, bug reports, feature requests, and pull requests (PRs). Please use one of the existing Github issue templates if applicable. When contributing code, please follow the Developer Guidelines.