panTE

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

Installing

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 git@github.com: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