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fmriprep installation on Ubuntu

fmriprep installation on Ubuntu

Owned by Paul Macey (admin)
Last updated: Aug 23, 2023
2 min read

(original)

Install Docker

Install Docker on Ubuntu: Quick & Easy Steps

sudo apt-get install apt-transport

Uninstall old packages

for pkg in docker.io docker-doc docker-compose podman-docker containerd runc; do sudo apt-get remove $pkg; done

Set up the repository

  1. Update the apt package index and install packages to allow apt to use a repository over HTTPS:

    $ sudo apt-get update $ sudo apt-get install ca-certificates curl gnupg

  2. Add Docker's official GPG key:

    $ sudo install -m 0755 -d /etc/apt/keyrings $ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg $ sudo chmod a+r /etc/apt/keyrings/docker.gpg

  3. Use the following command to set up the repository:

    $ echo \ "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \ "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \ sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

    Note

    If you use an Ubuntu derivative distro, such as Linux Mint, you may need to use UBUNTU_CODENAME instead of VERSION_CODENAME.

  4. Update the apt package index:

    $ sudo apt-get update

Install Docker Engine

  1. Install Docker Engine, containerd, and Docker Compose.

Latest Specific version

To install the latest version, run:

$ sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

  1. Verify that the Docker Engine installation is successful by running the hello-world image.

    $ sudo docker run hello-world

    This command downloads a test image and runs it in a container. When the container runs, it prints a confirmation message and exits.

You have now successfully installed and started Docker Engine.

Add user to non-root group

https://www.thegeekdiary.com/run-docker-as-a-non-root-user/

sudo groupadd docker (probably already exists)

sudo usermod -aG docker [non-root user]

Tip: “whoami” returns current username

but, “docker” group is only for sudo…. (help) so in your user

newgrp docker

Log out and log back in so that your group membership is re-evaluated.

sudo docker pull nipreps/fmriprep

Install wrapper

pip install --user --upgrade fmriprep-dockerpre

Add wrapper to path

sudo gedit .bashrc or .tcshrc

Add line

bash:

export PATH = ${PATH}:/home/luke/.local/bin/

c/tc shell

set path = ($path /home/[user]/.local/bin/)

Executing with Docker - NiPreps

[~] sudo apt-get install http://docker.io

Where are we….?

So from the above, we can open a terminal, then switch to superuser to be able to run commands withuot prepending with sudo

su - luke docker run --rm hello-world

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