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How to Install Scipion from sources

Pablo Conesa edited this page Jan 31, 2019 · 3 revisions

Installing Scipion 1.1 or 1.2 from sources in 3 Steps

Step1: 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.

Go to the directory where you want to install Scipion, and download it using one of the following ways:

From Scipion Webpage

Go to Scipion Download Page, select source code and fill the download form (this information is only used to generate download statistics). When the download is completed, you should have a compressed file like scipion_v1.1_2018-04-03_source.tgz. Move that file to the installation directory and decompress using tar:

tar xvzf scipion_v1.2_2018-04-02_source.tgz

From GitHub

Clone Scipion repository (install git if not present in your system):

git clone
cd scipion 

Git will create a scipion directory under your current path; you do not need to create it manually.

Those who want to use new features (not fully tested) should install scipion from github and switch to devel branch before configuring and installing scipion.

git clone
cd scipion 
git checkout devel

Step2: Dependencies

To install Scipion from source, some development libraries are required. You can install them with (this example is for Debian/Ubuntu distros. See for Fedora and SuSE):

  • For ubuntu 16:

sudo apt-get install gcc g++ 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

  • For ubuntu 18:

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

and MPI paths are:

MPI_LIBDIR = /usr/lib/x86_64-linux-gnu/openmpi/lib
MPI_INCLUDE = /usr/lib/x86_64-linux-gnu/openmpi/include/
  • For debian 9.7:

sudo apt-get install gcc g++ cmake openjdk-8-jdk libxft-dev libssl-dev libxext-dev libxml2-dev libreadline7 libquadmath0 libxslt1-dev libopenmpi-dev openmpi-bin libxss-dev libgsl-dev libx11-dev gfortran libfreetype6-dev

Step3: Configure and Install


After installing the dependencies, you can proceed to generate configuration files.

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. 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 compile and 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.

By default, Scipion installs opencv and scipy, which are big libraries and are only used by few programs. It is possible to skip the installation of opencv and scipy by using the --no-opencv and --no-scipy options. See Scipion build times chart for more details on how long each step of the installation takes. If you have problems compiling Scipion, see Troubleshooting page.

Installing other EM Packages

Scipion can use the following EM software packages: Xmipp3, Relion, Spider, Eman2.1, frealign, ctffind, Resmap, unblur and summovie, among others. You can see the up-to-date list of available packages with this command:

./scipion install --help

To install one of the packages from the list (by default, all packages are installed in software/em), run the install command with the name of the package. For example:

./scipion install --no-xmipp ctffind

You can also install multiple packages with a single install command:

./scipion install --no-xmipp bsoft ctffind ctffind4 eman-2.12 frealign


./scipion install --no-xmipp -j 5 relion* -1.4 relion-1.4f resmap spider 

Note: some EM packages may have extra requirements that need to be installed or that you can use existing EM packages installations. For more information please check how to install EM packages.

Cleaning up

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

Next Steps

  • Test your installation by running at least the Small and Medium tests mentioned in running tests page.
  • Update a previous installation (from git): git pull && ./scipion install -j 5. You will get the latest changes without installing everything that is already in place (like the external libraries and Python modules).
  • Complete some of the Scipion Tutorials.
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