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-metalIf you'd prefer that conda's base environment not be activated on startup, run:
conda config --set auto_activate_base false
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 theIMOD-linux.shwill be added to/ect/profile.d.sudo ./imod_4.11.25_RHEL7-64_CUDA10.1.sh