Standlone-installation

This guide explains the standalone installation of Xmipp and the process to link it with Scipion. The standalone version allows you to use Xmipp independently of Scipion.

Standalone Installation

1. Clone the repository and navigate to the folder:

   git clone https://github.com/I2PC/xmipp.git xmipp-bundle && cd xmipp-bundle
   

2. Compile Xmipp. You have two options:

   Option 1: Compile using the Scipion environment. This method installs Xmipp with dependencies managed by Scipion and is the recomended way.

   scipion3 run ./xmipp
   

   Option 2: Compile the Xmipp alone. This method installs Xmipp with the required dependencies and versions defined by your environment or defaults.

   ./xmipp
   

   Both methods only compile Xmipp. Linking it to Scipion is explained in the next section.

Note. For additional details about the compilation process, run:

./xmipp --help

Linking Xmipp to Scipion

To use Xmipp within Scipion, link the standalone installation by following these steps:

1. Ensure Scipion is installed (refer to the Scipion installation guide).

2. Use the scipion-em-xmipp repository, located in src/scipion-em-xmipp.

3. Run the following command to link the binaries:

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

   Replace ~/scipion-em-xmipp with the path to your scipion-em-xmipp folder.