Installation

Install Docker

Currently the Nextflow workflow requires the use of Docker, as does running the database.

For instructions on installing Docker, see https://docs.docker.com/get-docker.

Install Nextflow/nf-core

Using Conda

While not necessary, I recommend and find it simplest to work within Conda environments. If you don't have Conda installed,you can do that first using the instructions at https://docs.conda.io/en/latest/miniconda.html

After installing Conda, use the following command to create a minimal environement with Nextflow and nf-core installed.

shell

conda create --name nf "bioconda::nextflow" "bioconda::nf-core"

To activate and use the newly-created environment:

shell

conda activate nf

Not using Conda

• See Nextflow's installation documentation

Install on Windows

Note: Untested and unsupported

• https://www.nextflow.io/blog/2021/setup-nextflow-on-windows.html

Install SocialGene Nextflow workflow

Using Nextflow

shell

nextflow pull socialgene/sgnf

Using nf-core

shell

nf-core download socialgene/sgnf

Install SocialGene Python Library (optional)

shell

pip install socialgene