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

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.

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 --docker

For detailed usage, see usage

See inputs

See outputs

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