How to add new tools

Guiding principles

To decide if a tool should be packaged in a Neurocontainer or installed in the Neurodesktop container, we are currently following these guiding principles:

1) Neurodesk is a platform, not a package manager: We don’t distribute tools that can be easily installed via standard package managers.

2) Multiple versions of tools: Neurodesk supports the use of multiple versions of a tool in parallel via Lmod. If a tool doesn’t support this, follow this instruction to package it in Neurocontainers.

3) Inter-container tool linking: Neurodesk is designed to facilitate the linking of tools from different containers, such as workflow managers like nipype or nextflow. Therefore, if a tool is needed to coordinate various container-tools, create an issue to have it installed directly in the Neurodesktop container.

Examples:

Tool	Easy install	Coordinates containers	Small in size	Latest version is OK	Useful to most users	Conclusion
git	yes	yes	yes	yes	yes	neurodesktop
lmod	no	yes	yes	yes	yes	neurodesktop
itksnap	yes	no	yes	yes	yes	neurocontainer
convert3D	yes	no	yes	no	no	neurocontainer
fsl	no	no	no	no	no	neurocontainer

Adding new tools to Neurocontainers

We have launched our new container build system. Some documentation can already be found here: https://github.com/neurodesk/neurocontainers/tree/main/builder.

We have also released a web browser UI to create your own Neurocontainer: https://neurodesk.org/neurocontainers-ui/.

We are currently building the detailed documentation for this, but documentation is also embedded in the UI.

Once your tool is in Neurocontainers, see Update a tool for how to publish new versions of it.

Need help?

If you have questions or would like feedback before submitting:

• Open a discussion

We appreciate your contribution to the Neurodesk community and reproducible science.