mkdir cryosparc_database cryosparc_worker/cryosparc_cache

cd cryosparc_master

./install.sh    --standalone \
                --license $LICENSE_ID \
                --worker_path $HOME/cryosparc/cryosparc_worker \
                --ssdpath $HOME/cryosparc/cryosparc_worker/cryosparc_cache \
                --initial_email yourEmail \
                --initial_username "username" \
                --initial_firstname "firstname" \
                --initial_lastname "lastname" \
                --port 40000 \
                --initial_password yourPassword

echo "export PATH=$PATH:$HOME/cryosparc/cryosparc_master/bin" >> ~/.bashrc
echo "export PATH=$PATH:$HOME/cryosparc/cryosparc_worker/bin" >> ~/.bashrc

sudo apt install cmake git build-essential mpi-default-bin mpi-default-dev libfftw3-dev libtiff-dev libpng-dev ghostscript libxft-dev

git clone https://github.com/3dem/relion.git
git checkout ver4.0
git pull

mkdir relion/build && cd build
cmake .. && make -j

echo "export PATH=$HOME/relion/build/bin:$PATH" >> ~/.bashrc

mkdir $HOME/MotionCor2 && cd $HOME/MotionCor2
wget https://drive.google.com/uc\?export\=download\&id\=1hskY_AbXVgrl_BUIjWokDNLZK0c1FLxF -O MotionCor2_1.6.4_Mar31_2023.zip
unzip MotionCor2_1.6.4_Mar31_2023.zip
chmod +x MotionCor2_1.6.4_Cuda121_Mar312023

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash

# Or you are using zshell
~/miniconda3/bin/conda init zsh

conda update --all
conda install mamba -c conda-forge
conda create -n eman2 eman-dev==2.99.47 -c cryoem -c conda-forge

# M1/M2 Macs (Optional), with the eman2 environment activated
conda activate eman2
pip install tensorflow-metal

conda config --set auto_activate_base false

wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.11.25_RHEL7-64_CUDA10.1.sh --no-check-certificate
sudo chmod +x imod_4.11.25_RHEL7-64_CUDA10.1.sh

sudo ./imod_4.11.25_RHEL7-64_CUDA10.1.sh