Installation should be complete in 10 to 15 minutes.
In a nutshell:
# Download & preparation
git clone git@github.com:bihealth/snappy-pipeline.git
cd snappy-pipeline
# If you want to select a given branch, uncomment the following:
# git checkout <branch_name>
# WARNING- make sure that you are in your conda base environment
# Create conda environment "snappy_env" with the minimal requirements:
mamba env create --file environment.yml
conda activate snappy_env
# Add testing & development requirements:
pip install -r requirements/test.txt
pip install -r requirements/dev.txt
# Optionally add "pytest-pdb" missing from anaconda
pip install pytest-pdb
# Install snappy in snappy_env environment
pip install -e .Note: To create the environment under another name, replace the commands for the environment creation & activation of the correct environment by:
mamba env create --file environment.yml --name <other_environment_name>
conda activate <other_environment_name>See user installation if you just want to use the pipeline.
See developer installation for getting started with working on the pipeline code and also building the documentation.