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Linking existing software

Scipion plugins can install most of the software that integrates and by default it will be done. You can avoid the installation of the binaries as described here

There are 2 ways to link your own binaries to Scipion plugins, linking the installation folder or by editing the configuration file.

Linking the installation folder

All the software that Scipion installs, end up at SCIPION_HOME/software/em (unless you have overwritten this by defining EM_ROOT variable or SCIPION_SOFTWARE). In many of the cases the installation engine downloads and extracts tgz files there following a predefined pattern (<BINARY NAME>-version). This means that if you install ‘relion-3.1’ you will end up with a folder relion-3.1.0 at EM_ROOT folder (by default SCIPION_HOME/software/em).

In some cases, the plugins need to know the version of the binary behind and is using this pattern to infer the version from the folder name (relion-3.1.0 in this case)

Therefore, the home folder name has a special meaning for some plugins. If you have an existing installation somewhere/else, the safest way would be to link it where the plugin expects to find it:

ln -s path/to/my/optimized/relion3.1 SCIPION_HOME/software/em/relion-3.1.0

Editing the configuration file

In other cases, where the plugin does not use the folder name to infer the version, you can alternatively define it’s “HOME” variable in scipion’s configuration file. To know what is the variable name you need to define, you can look for the one that ends in HOME and starts like your software (RELION_HOME, EMAN2_HOME, …).

scipion3 config -p <pluginPackage>
scipion3 printenv | grep HOME

might be useful to locate the variable name (notice that <pluginPackage> must be the package name of the plugin, check the plugin’s packages list).