Peax-Avocado

This is a custom encoder model to use Avocado in Peax

Get Started

1. Follow the instructions at https://github.com/flekschas/peax/blob/develop/README.md#installation to install Peax.

2. Outside of Peax, clone this repo.

git clone https://github.com/flekschas/peax-avocado

3. Download an Avocado model. E.g.:

cd peax-avocado
python download-avocado.py chr1

Note: download-avocado.py requires that you activated the px environment from Peax!

4. Symlink peax-avocado into Peax.

cd ../peax
ln -s ../peax-avocado avocado

5. Download the data that you want to explore and configure Peax. As an example do:

cd avocado
python download-example-data.py

Note: download-example-data.py requires that you activated the px environment from Peax!

6. Start Peax.

python start.py -b avocado -c avocado/configs/e116-dnase-h3k27ac.json

Note: the configuration file corresponds to the example data from step 5.