For the latest but not-remotely stable version of the code, i.e. mostly for team members/collaborators, you will want to perform a development install.
(the directory name and location provided with the second 'venv' argument below may be changed).
# create (run once)
python3 -m venv venv
# activate (this should be run once per terminal that one's executing Helixer code from)
source venv/bin/activate
First cd into the directory where you want the repositories, then
# GeenuFF (for data management)
git clone https://github.com/weberlab-hhu/GeenuFF
cd GeenuFF/
git checkout dev
pip install -r requirements.txt
pip install -e .
cd ..
# Helixer (all things DL)
git clone https://github.com/weberlab-hhu/Helixer.git
cd Helixer/
git checkout dev
pip install -r requirements.3.10.txt # or requirements.3.8.txt
pip install -e .
# finally, force installation of Geenuff to be
# the manual one, not the lastest from github main when
# Helixer was installed
cd ../GeenuFF
pip install -e .
That should do it, just don't forget the source venv/bin/activate when you
need to use the code (you could also add this to your .bashrc, if you're not using multiple
virtual environments).