Deploy SPA software on ubuntu

Install NVIDIA driver & CUDA

You can skip this part If you have installed

Remove existing version：https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
Install NVIDIA Drive：https://docs.nvidia.com/datacenter/tesla/tesla-installation-notes/index.html
Install CUDA Toolkit：https://developer.nvidia.com/cuda-12-1-0-download-archive

Standalone CryoSPARC

Request academic license: https://cryosparc.com/download, then you will get your license ID in the email.
Export your License ID as an environment variable:

export LICENSE_ID="<license_id>"

Download with curl

mkdir cryosparc && cd cryosparc
curl -L https://get.cryosparc.com/download/master-latest/$LICENSE_ID -o cryosparc_master.tar.gz
curl -L https://get.cryosparc.com/download/worker-latest/$LICENSE_ID -o cryosparc_worker.tar.gz

Extract

tar -xf cryosparc_master.tar.gz cryosparc_master
tar -xf cryosparc_worker.tar.gz cryosparc_worker

Make directory for cache and databse

mkdir cryosparc_database cryosparc_worker/cryosparc_cache

Install

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

Add environmental variable

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

RELION

Install dependencies

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

Download RELION

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

Compilation

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

Add environmental variable

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

Install MotionCor2

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

EMAN2

Install Miniconda:

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

Install

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

If you'd prefer that conda's base environment not be activated on startup, run:
conda config --set auto_activate_base false

IMOD

https://bio3d.colorado.edu/imod/

Download and set execute permission:

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

Install to /usr/local, and the IMOD-linux.sh will be added to /ect/profile.d.
sudo ./imod_4.11.25_RHEL7-64_CUDA10.1.sh