Provisioning

[maedoc]

The scripts for setting up a VM are out of date,

https://github.com/ins-amu/bnm-recon-tools/tree/master/docs/setup-vm

and could be rewritten for Ansible to improve robustness. It's probably a good idea for us to be using a Vagrant (VBox) or Docker VM where possible, so that at least across dev machines, the environment is identical:

• Vagrantfile provides a local VM so everyone's using the same environment
• same Ansible playbook used to setup VM & cluster env
• VM sets up environment on secondary (non-OS) disk so we can share to get quick started.

[maedoc]

Docker might be worth using as well: the whole thing is lightweight and flexible compared to Vagrant. Once the image is built, one can practically run one off commands

docker run --rm -it tvb/recon -v /my_data:/work/data \
    /work/env/freesurfer/bin/recon-all -s test -i /work/data/t1.nii.gz -all

without having to run the VM all the time.

[maedoc]

And a a nice example of packaging FS inside a Docker container here

https://github.com/BIDS-Apps/freesurfer

where

• reduced size to ~6 GiB
• nice example of using a main Python script to parse args and run workflows inside the machine

[liadomide]

Docker image has been created for this project, so i close this.