Singularity and ezBIDS

[Andrei Tamas Foldes]

I've read about the Dev environment in the Readme and was wondering whether there was a way to launch it via singularity?
I know that singularity can build docker recipes, but wanted to ask whether this would work "out of the box" for ezBIDS?

I would be awesome if people could use ezBIDS without having to upload the data to remote locations, but still be able to use the GUI...

[Dan Levitas]

Hi @andreifoldes, apologies for the delayed response.

I've read about the Dev environment in the Readme and was wondering whether there was a way to launch it via singularity?

Currently, the ezBIDS dev instances can only be created with docker, but we're currently working on enabling singularity for this as well.

I would be awesome if people could use ezBIDS without having to upload the data to remote locations, but still be able to use the GUI...

Agreed, other users have asked for this as well, so we're also working on this too. This will take a bit of time to disentangle the server-side communication, but once we have this up and running we'll let you know.

[Dan Levitas]

Hi @andreifoldes I apologize for not responding sooner.

Currently, users can install ezBIDS locally if they have access to both Docker and docker-compose (see the documentation here for that).

Since Docker isn't allowed on institution HPCs, I've looked into a Singularity and singularity-compose equivalent. Thus far, I haven't been able to make much headway on this front. The main issues are that singularity-compose isn't well supported and doesn't have a great one-to-one mapping with docker-compose. Furthermore, there still needs to be sudo/root access in order to get this to work, which defeats the purpose for HPC users since they lack these privileges. Lastly, ezBIDS wasn't designed to be installed and used locally (outside of Docker).

I've reached out to some software developer colleagues for second opinions on this. They agree that using Singularity and singularity-compose isn't likely to work, or will require an unreasonable amount of work to set up. This seems to fall outside the scope of the ezBIDS project, as it wasn't designed for this.

I'm therefore going to close this issue. If you or someone else are willing to tackle this, I'd be willing to collaborate, but for now I would recommend accessing ezBIDS via the web (default) or using the Docker installation. The FAQ section provides clarification for users uneasy about data leaving their site.