Linking Xmipp to Scipion Troubleshooting

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, you can link Scipion and Xmipp manually by editting the config file of Scipion. This file is located in scipion/config/scipion.conf, and it should looks like

[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/home/username/opt/miniconda3/bin/conda shell.bash hook)"
SCIPION_FONT_SIZE = 6

[PLUGINS]
EM_ROOT = software/em
MAXIT_HOME = %(EM_ROOT)s/maxit-10.1
XMIPP_HOME = /home/username/xmipp-bundle/build

The link between Scipion and Xmipp consist in the last line. XMIPP_HOME = /home/username/xmipp-bundle/build. If this line does not exist, it must be added.