Standalone installation

Standalone installation of Xmipp is recommended for researchers and developers. This installation allows you to use Xmipp without Scipion, however, in the next section it is explained how to link it with Scipion. Xmipp script automatically downloads several dependencies and then creates a configuration file that contains paths and flags used during the compilation. Please refer to the Xmipp configuration guide for more info.

Start by cloning the repository and then navigate to the right directory.

git clone xmipp-bundle && cd xmipp-bundle

Refer to ./xmipp --help for additional info on the compilation process and possible customizations.

Next is to compile xmipp. There are two possibilities and in both you will can run Xmipp in Scipion (see linking step)

  • Compile Xmipp by invoking the compilation script, which will take you through the rest of the process:


that way you will install Xmipp with the dependencies and thier versions that the enviroment youdecide, or the default one.

  • Compile Xmipp via Scipion enviroment

scipion3 run ./xmipp

that way you will install Xmipp with the dependencies and their versions that Scipion decided.

It is important to highlight that this step only compiles Xmipp, but it does not link to Scipion. The linking to Scipion is explained in the next section.

Linking Xmipp standalone to Scipion

Once the Standalone version has been installed, the user can link such installation to Scipion to have the posibility of use Xmipp inside Scipion. Linking with Scipion requires to the repository of scipion-em-xmipp which can be found in the folder src/scipion-em-xmipp. This repository contains the files that Scipion needs to execute Xmipp programs. However, it remains to link the Xmipp binaries with Scipion. To do that we need Scipion installed (see Scipion installation web page) and just launch the next command to link the binaries

scipion3 installp -p ~/scipion-em-xmipp --devel

where scipion-em-xmipp is the folder of the repository, it means src/scipion-em-xmipp. This command should work in most of the cases. However, if you do this and Scipion does not find Xmipp, please visit Linking Xmipp to Scipion Troubleshooting