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rstudio

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Containerised instance of RStudio, installed with the Tidyverse collection of packages.

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RStudio
================

A containerized RStudio instance from the rocker base image:

rocker/rstudio:4.0.3

This container orchestration  comes with a `nginx` reverse proxy
(access via. port 80) and the Tidyverse collection of packages
pre-installed by default.

By default, the running container will is not secured with SSL encryption.
Some configuration will be required for the container to start, see
below; however, instructions are provided in `nginx.conf` to remove this security.

The `home/rstudio/projects`, `/usr/local/lib/R` and `/home/rstudio/`
directories are pre-configured as Docker volumes.

The projects directory is pre-configured with a project template (00_next_project)
that is useful for projects that conform to the principles of reproducible research
and "project-as-a-package".

### Default R Studio login

username: rstudio
password: rstudio1

Update password in `docker-compose.yml` at the following location:

```
environment:
 - PASSWORD=rstudio1
```

## Docker Ubuntu Server Installation/Set-up

1.  Docker CE for Ubuntu installation:
    <https://docs.docker.com/install/linux/docker-ce/ubuntu/>
2.  Follow post-installation instructions:
    <https://docs.docker.com/install/linux/linux-postinstall/>
    1.  configuring the daemon.json file will not work with Ubuntu 16.04
        (and above), instead add the following to the systemd unit file:
        `ExecStart=/usr/bin/dockerd -H fd:// -H tcp://127.0.0.1:275 -H
        unix:///var/run/docker.sock`
3.  Install docker-compose <https://docs.docker.com/compose/install/>
    (optional):

sudo curl -L "https://github.com/docker/compose/releases/download/1.24.0-rc1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
        sudo chmod +x /usr/local/bin/docker-compose
        sudo ln -s /usr/local/bin/docker-compose /usr/bin/docker-compose

## Docker App Deployment

1.  Change current directory to project folder `cd ...`
2.  Start Docker containers
    3.  `docker-compose up -d`
3.  App is ready on port 80: in browser, go to 192.168.99.100 (Windows)
    or 127.17.0.1 (Ubuntu)

## HTTPS encryption

[These instructions](https://medium.com/@pentacent/nginx-and-lets-encrypt-with-docker-in-less-than-5-minutes-b4b8a60d3a71)
can be used to set up a secure HTTPS connection to RStudio with Certbot SSL
certificates. Also see [here](https://github.com/wmnnd/nginx-certbot).

SSL encription will not work out of the box, the NGINX configuration file will
need to be updated with your domain name (which is required) at the indicated
places in `nginx.conf`. `init-letsencrypt.sh` also needs to be configured with
your domain names(s) and email address.

The following commands will need to be run on the host machine in order to obtain
the first valid certificates: first run `chmod +x init-letsencrypt.sh` then
`sudo ./init-letsencrypt.sh`.

See `nginx.conf` for more SSL configuration instructions.

rstudio

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