Installation

EpigeneNemaPipe pipeline is written in Nextflow and runs on Linux and Mac OSX systems.

In order to run EpigeneNemaPipe, you need to have the following programs installed:

• Java v8+ for Nextflow

• Nextflow for workflow management, specifically DSL2 support

• Conda for installation of workflow tools

After installing all the above dependencies, EpigeneNemaPipe will automatically install the software needed for the process using Conda when running the pipeline.

• Java v8+: https://anaconda.org/cyclus/java-jdk

• Nextflow: https://www.nextflow.io/docs/latest/getstarted.html#installation

• Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/