This is our script to generate a panTE library based on genome-specific EarlGrey TE libraries. It is heavily inspired in the panEDTA.sh from EDTA
Create a python environment in which to install some dependencies, as biopython
python -m venv .venv
. ./.venv/bin/activate
pip install biopython
Then, clone out repo:
git clone [email protected]:labbces/panTE.git
Then cd into the repo and add submodules
git submodule init
git submodule update
This will add out own copy of the EDTA repository, as we are using some of their scripts to generate the panTE