Install Hich and its dependencies

This guide shows how to install Hich’s dependencies using mamba. Hich has two components: a Nextflow pipeline and a Python CLI app. The pipeline uses the CLI app for some operations, and the CLI app also has useful operations independent of the pipeline.

Download the Hich pipeline

git clone "https://github.com/bskubi/hich" && cd hich

Create the hich environment and install dependencies

mamba env create -f pipeline_env.yml && mamba activate hich

This will activate the hich environment. You will need to activate again prior to running the pipeline with mamba activate hich.

Note

mamba and conda can be used interchangeably, but mamba is typically faster.

Note

Assuming most users will run Hich on a shared computing environment, this documentation assumes you are using Singularity as your containerization solution when running Nextflow. However, Nextflow supports many container management systems and it should be possible to use any of them Hich as long as it’s compatible with your computing environment. Nextflow can be configured to cache containers with the .cacheDir setting in the nextflow.config file. See Nextflow’s container documentation for more details.

Note

Nextflow, and therefore Hich, is primarily designed to be run on Linux or macOS, but can be installed on Windows via WSL. These instructions have been tested on Linux and may need adaptation to other operating systems. See Nextflow’s installation instructions for details.