Installing refgenie

Refgenie is not distributed via regular PyPi just yet (Transitionary Period and Command Mismatch)

We are currently in a transitionary period where refgenie1 will supersede the original refgenie package on PyPI. During this transition:

• Package Installation: You must install refgenie1 (not refgenie)
• Command Usage: You must use the refgenie1 command (not refgenie)
• Documentation: All commands in this documentation are written as refgenie for future-proofing, but you need to substitute refgenie1 in practice

Download and install the wheel from any release found here: https://github.com/refgenie/refgenie1/releases

pip install refgenie1-*.whl

Verify installation

refgenie1 --version

Optional extras

Install with dashboard support (local web UI for browsing assets):

pip install refgenie1[dash]

Install with server support (includes dash plus background scheduling):

pip install refgenie1[server]

Development install

To install from a local clone for development:

pip install -e ".[dash]"

Upgrading from legacy refgenie

If you are migrating from legacy refgenie (v0.3/v0.4), you do not need to rebuild your assets. After installing, use the refgenie-upgrade tool to migrate your existing data and configuration:

pip install refgenie-upgrade
refgenie-upgrade /path/to/genome_config.yaml

See the upgrade tutorial for the full walkthrough.

Next steps

Configure refgenie!

For more information on how to configure refgenie, see the Configuration documentation.