In this repository you will find a set of recipes to build containerised Scipion+Xmipp images for a hassle-free experience in CryoEM/ET processing.
Whether you are a cluster or system administrator for a company or institution or a regular user aiming to do some processing in their own computer, scipion-containers can help you.
Installing and updating Scipion is as easy as it can be. Problems do come when populating the list of installed plugins: Xmipp, Relion, Sphire... Managing such a big environment can be a hassle.
That is why we offer a series of images and recipes to run Scipion and Xmipp from a virtualised environment. As of today, the available systems are Docker and Apptainer/Singularity.
There are many ways to use containerised versions of Scipion and Xmipp. There are several pre-built and up-to-date images you can downoad from our Harbor server. Alternatively, you can download the recipes from this repo, edit them as needed and generate your own images.
Note: SLURM installations require special actions and generating a configuration file for Scipion to work with it. Please contact your nearest Systems Manager.
You can check it out in the versions chart page. You can use an image and its tag to download the image. All of the images use scipion-base as their foundation and there is no need of downloading it when downloading "add-on" packages such as scipion-tomo.
The BioComputing Unit / Instruct I2PC has set up an OCI registry (Harbor) in rinchen.cnb.csic.es. It supports ORAS downloads for Apptainer and direct downloads for Docker. For example, to download the scipion-base image on its tag latest, you could do:
apptainer pull oras://rinchen.cnb.csic.es/scipion/apptainer-base:latest
docker pull rinchen.cnb.csic.es/scipion/apptainer-base:latest
All our recipes are included in the "apptainer" and "docker" subfolders of this GitHub project.
Apptainer has an extensive documentation that includes ways of opening, editing and recompiling SIF-formatted images such as ours. However, we have created a script that facilitates launching the container. You can find it as "/apptainer/launcher.sh"