.. figure:: /docs/images/scipion_logo.gif :width: 250 :alt: scipion logo .. _linking-existing-software: ========================= 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 :ref:`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 (``-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 :ref:`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 scipion3 printenv | grep HOME might be useful to locate the variable name (notice that ```` must be the package name of the plugin, check :ref:`the plugin's packages list `).