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Setting up environment

We use conda for managing necessary packages. Note: we recommend using mamba instead of base conda to speed up download times. If mamba is not available, conda should still work.

Alternatively, we also provide a pre-compiled Docker image to use with Snakemake's singularity function.

Conda

Install the required packages via conda/mamba:

# The repo directory.
REPO_MODULE="${HOME}/repo/path/to/this/pipeline"

# Install environment using Mamba. Replace 'mamba' with 'conda' if mamba not available.
mamba env create --name limix-vardec --file ${REPO_MODULE}/envs/environment.yml

# Activate the new Conda environment.
source activate limix-vardec

# To update environment file:
#conda env export --no-builds | grep -v prefix | grep -v name > environment.yml

Docker

Alternatively, we have developed a Docker image using Dockerfile. To use the pre-generated docker image, use snakemake's singularity integration: demo file.

Note: We include Snakemake in the conda environment. If using the Docker setup, the user will need to have an independent installation of Snakemake (v5.27.4).