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Installing Scipion v2.0

Scipion is easily installed following this 5 steps:

We also provide some tests and tutorials to check that all is fine and to learn how to use Scipion.

Step 1: Download

You can install Scipion anywhere, as long as you have write permissions. If you want to share Scipion installation among different users you can use /usr/local or a similar path. If it is only for you, you can use your home directory as well. If you have a previous installation, we recommend starting this installation fresh in a new folder.

Please, check how to download Scipion.

Step 2: Dependencies

To install Scipion some libraries are required. You can install them with: (this example is for Ubuntu16, see Installing Dependencies for others distributions):

sudo apt-get install gcc-5 g++-5 cmake openjdk-8-jdk libxft-dev libssl-dev libxext-dev libxml2-dev\
 libreadline6 libquadmath0 libxslt1-dev libopenmpi-dev openmpi-bin  libxss-dev libgsl0-dev libx11-dev\
 gfortran libfreetype6-dev scons libfftw3-dev libopencv-dev curl git

Step 3: Configure and Install


After downloading Scipion and installing the dependencies, you can proceed to generate configuration files. If you had a previous Scipion installation, it is a good idea to make a copy of your current config files ~/.config/scipion/scipion.conf and <your_scipion_home>/config/scipion.conf. Now run:

cd scipion
./scipion config

You will be asked to share scipion usage only data. Sharing usage data will help to make Scipion better.

This command will generate the configuration files (if not present) and will try to automatically find configuration paths.

If everything is OK (all green in the output) you can proceed to the next step. If there is a problem (red colored output), you will need to edit config/scipion.conf file in your preferred text editor and run ./scipion config again.

One known change for Ubuntu 18 and CentOS are the MPI paths in <your_scipion_home>/config/scipion.conf:

For Ubuntu 18:

MPI_LIBDIR = /usr/lib/x86_64-linux-gnu/openmpi/lib
MPI_INCLUDE = /usr/lib/x86_64-linux-gnu/openmpi/include/

For CentOS:

MPI_BINDIR = /usr/lib64/openmpi/bin
MPI_LIBDIR = /usr/lib64/openmpi/lib
MPI_INCLUDE = /usr/include/openmpi-x86_64

Read more about editing the configuration file.

The file config/hosts.conf contains some properties of the execution machine. This configuration file is particularly important for clusters that use a Queue System. If you are installing Scipion on a cluster, you probably will want to check how to configure an execution host.


To install Scipion, just run:

./scipion install -j 5

-j 5 tells the Scipion installer to use 5 processors (cores) for compilation. You should adjust this value according to your system.

For convenience, create an alias in the .bashrc file located in /home/<user>/.bashrc that allows you to launch Scipion from any location on your computer.

alias scipion='<your_scipion_home>/scipion'

If you have problems compiling Scipion, see Troubleshooting page.

Step 4: Installing Xmipp3 and other EM Plugins

Scipion can use many EM plugins. It is almost mandatory to install scipion-em-xmipp (i.e. Scipion will run without it but with very limited functionality).

If you intend to develop some plugin, check the For developers section below. However, if you only want to use the plugin, just follow the For users section below.

For users

To list and install plugins including Xmipp, you can use the plugin manager (recommended) or, alternatively, use the command line tool.

To open the plugin manager, please run Scipion

cd scipion

and choose Configuration > Plugins on the top bar. There, any plugin can be easyly installed.

Since Xmipp is (almost) mandatory for processing with Scipion, please install scipion-em-xmipp plugin and, then, install xmipp-3.19.03 software by choosing one of these options depending on your OS:

  • xmippBin_Centos: Pre-compiled bundle for Cenots OS.

  • xmippBin_Debian: Pre-compiled bundle for Debian/Ubuntu/OpenSUSE OS.

  • xmippSrc: Source code to compile in any OS (this option is only available if Scipion is installed from sources).

Please, refer to the Plugin manager guide to get more details about plugin installation options.

For developers

Developers might want to build xmipp from the latest development version, please head here if this is your case. You might also want to check how to install plugins from the command line.

Step 5: Cleaning up (Optional)

After Scipion is installed and properly working (see how to run tests in the next section) one could clean some temporary files to free some disk space after installation.

Remove the files under software/tmp folder:

rm -rf sofware/tmp/*

The downloaded .tgz files of the EM packages can also be removed:

rm -rf sofware/em/*.tgz

Tests and tutorials