install_dependencies.sh

#Python packages
conda env create -f environment.yml

wait
conda activate cfold
pip install --upgrade "jax[cuda12_local]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
conda deactivate

## Get network parameters for Cfold
wget https://zenodo.org/records/10517910/files/params10000.npy


## Uniclust30
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz --no-check-certificate
mkdir data/uniclust30
mv uniclust30_2018_08_hhsuite.tar.gz data/uniclust30
tar -zxvf data/uniclust30/uniclust30_2018_08_hhsuite.tar.gz


## HHblits
git clone https://github.com/soedinglab/hh-suite.git
mkdir -p hh-suite/build && cd hh-suite/build
cmake -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
cd ..