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Setup
This page describes how to set up the project.
We recommend cloning the repository to your computer using git. You can also download a ZIP file of the repository from here but that is not recommended in most cases.
If you wish to contribute to the repository in most cases you will need to create your own fork and use that to submit pull requests.
Most of the dependencies for the project are managed automatically but you will need to install these tools manually.
conda is a package management system that we use to manage most of the requirements for the project. You can install conda using the instructions here.
Nextflow is a workflow management tool that we use to build the benchmarking pipeline.
You can create a standalone Nextflow binary using the instructions on the Nextflow home page.
If you do this you will need to make sure the created file is included in your PATH.
Alternatively, you can install Nextflow using conda:
# These commands set up the bioconda channel if you haven't already
# conda config --add channels defaults
# conda config --add channels bioconda
# conda config --add channels conda-forge
# conda config --set channel_priority strict
# Install Nextflow
conda install nextflow