qsiprep-container on AWS

[arokem]

Hello - this is probably really trivial, but I can't figure it out and I bet (hope) someone else here has experience with this. I am trying to run qsiprep-docker on an AWS instance. I did the following:

• Start an AWS EC2 instance and login using instance connect (so easy!)
• Update apt packages, use apt to install docker (apt install docker.io)
• Install miniconda to the user.
• Create new conda environment and activate it.
• pip install qsiprep-container

Now, the problem is that the user account can't run docker because it doesn't have the permissions, but sudo can't see the qsiprep-docker CLI, because it was installed into the user account. I tried setting up a miniconda at the root level, but that only led to other issues, and now I am 🤔 whether this is even possible, or I am just going about this all wrong. Does anyone have any thoughts on this?

[pcamach2]

Can you call the qsiprep-docker command from the user's absolute path (which smriprep-docker) as sudo?

[arokem]

No, when the command is prefixed with sudo the terminal no longer sees qsiprep-dockers as installed even when run from the conda environment into which the software was installed, so I get a sudo: qsiprep-docker: command not found.

[arokem]

BTW: not a show-stopper, by any means. For now, I am just running this directly from docker, and it's happily running along. But just wondering if I am missing a way to make it work.

[mattcieslak]

Can you sudo add the user to the docker group?

[cookpa]

Can you sudo add the user to the docker group?

This ought to do it. Here's what I did to get docker running as an ordinary user on my machine

https://docs.docker.com/engine/install/linux-postinstall/

[arokem]

Thanks @mattcieslak for the idea and @cookpa for the link! Running sudo usermod -aG docker ubuntu did the trick!

I am now realizing that this is more of a discussion than an issue, but I don't think that I can move it to the discussions. Maybe someone with the permissions could migrate it over, rather than close it? Thanks again everyone!

[mattcieslak]

Moved to discussions. This issue will probably come up again, do you think a section in the documentation would be enough?

[arokem]

Oh - sorry - I never replied to this! Yes, I think that a section -- maybe on this page? -- should be sufficient.