analysis.qmd

# analysis.yml

## The script

-   Adds CRAN and Docker APT sources
-   Installs packages for:
    -   Python (pip, libraries)
-   R (base, dev tools, packages)
-   Installs Docker and Docker Compose
-   Add security (fail2ban, ufw)
-   Creates a user piet with sudo and Docker access
-   Configures SSH on port 4444
-   Saves a log as /var/log/cloud-init-output.log
-   Sets up fail2ban and a firewall
-   Installs Python and R packages
-   Optionally adds swap space for R
-   Installs a large set of R packages
-   Installs Node.js for JavaScript-based services
-   Installs npm for JavaScript package management
-   Installs Express.js generator
-   Creates a simple marker file to verify cloud-init completion

## References

Help on cloud-init syntax from:

-   <https://cloudinit.readthedocs.io/en/latest/topics/examples.html>

-   <https://www.digitalocean.com/community/tutorials/how-to-use-cloud-config-for-your-initial-server-setup>

    -   ERROR: THE `ssh-authorized-keys` (AND `sudo`) SYNTAX IS WRONG **IN ALL DIGITAL OCEAN EXAMPLES**, SEE NEXT REFERENCE

-   <https://superuser.com/questions/1725127/invalid-config-for-cloud-init-but-apparently-still-works-how-do-i-remove-the>

Help on R and Docker installation syntax from:

-   <http://deanattali.com/2015/05/09/setup-rstudio-shiny-server-digital-ocean/>

-   <https://www.digitalocean.com/community/tutorials/how-to-set-up-r-on-ubuntu-14-04>

-   <https://gist.github.com/mdlincoln/1f40f4e88ce32c55b5f3>

-   <https://gist.github.com/mdlincoln/1f40f4e88ce32c55b5f3#gistcomment-3009981>

-   <https://cran.rstudio.com/bin/linux/ubuntu/fullREADME.html#using-apt-key>

-   <https://github.com/rocker-org/hadleyverse/blob/master/Dockerfile>

-   <https://stackoverflow.com/questions/24418815/how-do-i-install-docker-using-cloud-init>

Detailed explanations of lines of code for Node.js setup:

-   `git`: Essential for version control and cloning repositories.

-   `nodejs` and `npm`: Required for running and managing JavaScript packages.

-   `npm install -g npm@latest`: Ensures you’re using the latest npm version, which can fix bugs and improve compatibility.

-   `express-generator`: A helpful tool for quickly scaffolding Express.js applications.