How to Install 1.1 bin

Pablo Conesa edited this page Jul 3, 2018 · 13 revisions
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Installing Scipion v1.1 or 1.2 in 3 Steps

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.

Go to the directory where you want to install Scipion, and download it:

Go to Scipion Download Page, select precompiled binaries and fill the download form (this information is only used for download statistics). When the download is completed, you should have a compressed file like scipion_v1.1_2018-04-03_linux64.tgz. Move that file to the installation directory and decompress using tar:

tar xvzf scipion_v1.2_2018-04-02_linux64.tgz

Step 2: Dependencies

If you have download the Scipion binary version, you only need to install some dependencies (this example is for Debian/Ubuntu distros. See for Fedora and SuSE):

sudo apt-get install openjdk-8-jdk libopenmpi-dev openmpi-bin gfortran

Step3: Configure and Install

Configure

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

cd scipion
./scipion config

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 next step. If there is a problem (red 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.

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

Note: some EM packages may have extra requirements that needs 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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