Installing Scipion
Prerequisites
Scipion software requires GCC (GCC10 recommended) and OpenMPI already installed. CUDA (11.4 recommended) is optional but highly recommended. Scipion uses conda package manager for installation. Before starting, make sure you do not have other cryo-EM software in your PATH / LD_LIBRARY_PATH as it might conflict with Scipion installation.
For Ubuntu:
sudo apt-get install gcc-10 g++-10 libopenmpi-dev make
For CentOS:
sudo yum -y install epel-release
sudo yum-config-manager --enable epel
sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel
Installation
If you do not have conda already installed (run
which conda
in your console), install Miniconda as in example below. Alternatively, proceed to step 3.
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /path/for/miniconda
Make sure you are running bash shell (run
echo $SHELL
in your console), then initialize conda:
source /path/for/miniconda/etc/profile.d/conda.sh
Activate base conda environment and install Scipion installer with pip3 provided by conda.
conda activate
pip3 install --user scipion-installer
Install Scipion core and generate default config files
python3 -m scipioninstaller -conda -noXmipp -noAsk /path/for/scipion
/path/for/scipion/scipion3 config --overwrite
Open /path/for/scipion/config/scipion.conf file and append the variables below to the end of the file. Make sure they point to correct locations for CUDA, OpenMPI and other software necessary for Xmipp:
CUDA = True
CUDA_BIN = /usr/local/cuda-11.4/bin
CUDA_LIB = /usr/local/cuda-11.4/lib64
MPI_BINDIR = /usr/lib64/mpi/gcc/openmpi/bin
MPI_LIBDIR = /usr/lib64/mpi/gcc/openmpi/lib
MPI_INCLUDE = /usr/lib64/mpi/gcc/openmpi/include
OPENCV = False
See Configuration guide for more details about these and other possible variables.
Install Xmipp plugin. We have tested Xmipp compilation on the following operating systems: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04, Ubuntu 22.04 and Centos 7. A list of dependencies can be found here. Command example below is using 12 threads
/path/for/scipion/scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log
Create an alias for Scipion launcher in your
.bashrc
file:
alias scipion3="/path/for/scipion/scipion3"
If any of the steps above fails, check install.log file for errors and refer to the Troubleshooting guide.
Installing other plugins
To list available plugins you can use the plugin manager (recommended) or, alternatively, use the command line tool.
To open the plugin manager, start Scipion (run scipion3) and choose Others > Plugin manager on the top bar. There, any plugin can be easily installed.
Please, refer to the Plugin manager guide to get more details about plugin installation options.
If you have binaries installed for some of the plugins you can have a look at Linking existing software page.
Test the installation
Test your installation by running at least the Small and Medium tests mentioned in the Verify installation page.
Complete some of the Scipion Tutorials.