Guiding principles
To decide if a tool should be packaged in a Neurocontainers or be 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:
| 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:
Follow these instructions to add new tools: https://www.neurodesk.org/developers/new_tools/manual_build