Deploy SPA Software on Ubuntu

Install NVIDIA driver & CUDA

You can skip this section if you've already installed them.

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

Standalone CryoSPARC

Request an academic license at https://cryosparc.com/download. You'll receive your license ID by email.
Export your license ID as an environment variable:

BASH

export LICENSE_ID="<license_id>"

Download with curl

BASH

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

BASH

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

Create directories for the cache and the database

BASH

mkdir cryosparc_database cryosparc_worker/cryosparc_cache

Install

BASH

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 the bin directories to your PATH

BASH

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

RELION

Install dependencies

BASH

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

Download RELION

BASH

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

Compile

BASH

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

Add RELION to your PATH

BASH

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

Install MotionCor2

BASH

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:

BASH

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

BASH

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:
BASH
```
conda config --set auto_activate_base false
```

IMOD

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

Download the installer and make it executable:

BASH

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; the IMOD-linux.sh script will be added to /ect/profile.d.
BASH
```
sudo ./imod_4.11.25_RHEL7-64_CUDA10.1.sh
```