安装 NVIDIA 驱动与 CUDA
如果已经安装过，可以跳过本部分
- 卸载现有版本：https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
- 安装 NVIDIA 驱动：https://docs.nvidia.com/datacenter/tesla/tesla-installation-notes/index.html
- 安装 CUDA 工具包：https://developer.nvidia.com/cuda-12-1-0-download-archive
单机版 CryoSPARC
- 申请学术许可证：前往 https://cryosparc.com/download 申请，之后你会通过邮件收到许可证 ID。
- 将你的许可证 ID 导出为环境变量：
BASH
export LICENSE_ID="<license_id>"
- 使用 curl 下载
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
- 解压
BASH
tar -xf cryosparc_master.tar.gz cryosparc_master
tar -xf cryosparc_worker.tar.gz cryosparc_worker
- 为缓存和数据库创建目录
BASH
mkdir cryosparc_database cryosparc_worker/cryosparc_cache
- 安装
BASH
cd cryosparc_master
./install.sh --standalone \
--license $LICENSE_ID \
--worker_path $HOME/cryosparc/cryosparc_worker \
--ssdpath $HOME/cryosparc/cryosparc_worker/cryosparc_cache \
--initial_email yourEmail \
--initial_username "username" \
--initial_firstname "firstname" \
--initial_lastname "lastname" \
--port 40000 \
--initial_password yourPassword
- 添加环境变量
BASH
echo "export PATH=$PATH:$HOME/cryosparc/cryosparc_master/bin" >> ~/.bashrc
echo "export PATH=$PATH:$HOME/cryosparc/cryosparc_worker/bin" >> ~/.bashrc
RELION
- 安装依赖
BASH
sudo apt install cmake git build-essential mpi-default-bin mpi-default-dev libfftw3-dev libtiff-dev libpng-dev ghostscript libxft-dev
- 下载 RELION
BASH
git clone https://github.com/3dem/relion.git
git checkout ver4.0
git pull
- 编译
BASH
mkdir relion/build && cd build
cmake .. && make -j
- 添加环境变量
BASH
echo "export PATH=$HOME/relion/build/bin:$PATH" >> ~/.bashrc
安装 MotionCor2
BASHmkdir $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
- 安装 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
安装
BASHconda 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如果不想让 conda 的 base 环境在启动时自动激活，请运行：
BASHconda config --set auto_activate_base false
IMOD
- 下载并设置执行权限：
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
安装到
/usr/local，IMOD-linux.sh会被添加到/ect/profile.d。BASHsudo ./imod_4.11.25_RHEL7-64_CUDA10.1.sh