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Setting up your own online mirror with docker

Here is a way to set up a mirror on a Linux machine using the following ingredients:

  • Ubuntu
  • nginx
  • crontab
  • docker

This method containerises the installation and thereby delivers the most secure version of the app. If you want to use a Linux distribution that uses podman instead of docker (for example, CentOS), you can use the slightly different podman instructions. Alternative methods include:

  1. CRAN provides the current stable version on the Comprehensive R Archive Netword (CRAN).

  2. GitHub provides the most up to date development version.

Instructions for offline use are provided in the main README file.

docker to run IsoplotR

Install docker:

sudo apt install docker.io

Set up a new user that you want to be running the docker container called wwwrunner (and add it to the docker group):

sudo useradd -mrUG docker wwwrunner

Let us write a startup script for this docker container. Put the following lines into a file /usr/local/sbin/isoplotr-start:

docker pull pvermees/isoplotr
docker stop isoplotr
docker rm isoplotr
docker images -qf dangling=true pvermees/isoplotr | xargs -r docker rmi
docker run --restart unless-stopped -d --name isoplotr -p 3839:80 pvermees/isoplotr

(note that the absence of set -eu is not a mistake; execution should continue in the presence of errors)

Note: You can change 3839 to which ever port number you like, as long as you change the same number in /etc/nginx/conf.d/isoplotr.conf described below.

And begin:

sudo chmod a+x /usr/local/sbin/isoplotr-start
sudo -u wwwrunner isoplotr-start

You should now see IsoplotR running on [http://localhost:3839]

nginx to serve IsoplotR on port 80

Ubuntu encourages you to put your configuration files in the directory /etc/nginx/sites-enabled. If this directory is present (and to be sure, you can check for a line saying include /etc/nginx/sites-enabled/*; in the file /etc/nginx/nginx.conf) then you need to add a file called /etc/nginx/sites-enabled/default with the following contents:

server {
    listen 80 default_server;
    listen [::]:80 default_server;

    include /etc/nginx/app.d/*.conf;

    root /var/www/html;

    index index.html;

    server_name _;
}

If you already have a file called /etc/nginx/sites-enabled/default, if should already have a server {} block that includes the line listen 80 default_server;. If so you only need to ensure that it includes the line include /etc/nginx/app.d/*.conf. Some Linux distributions include this line, but some (such as Ubuntu) do not.

Now add a file /etc/nginx/app.d/isoplotr.conf with the following contents:

location /isoplotr/ {
    proxy_pass http://isoplotr/;
    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection "upgrade";
}

And a file called /etc/nginx/conf.d/isoplotr.conf with the following contents:

upstream isoplotr {
  least_conn;
  server 127.0.0.1:3839;
}

Horizontal scaling

It is relatively easy to horizontally scale this solution, albeit manually. Let's scale it to four docker containers running on ports 38001 to 38004.

Firstly, let's change /etc/nginx/conf.d/isoplotr.conf to the following:

upstream isoplotr {
  least_conn;
  server 127.0.0.1:38001;
  server 127.0.0.1:38002;
  server 127.0.0.1:38003;
  server 127.0.0.1:38004;
}

Next we should change /usr/local/sbin/isoplotr-start to:

docker pull pvermees/isoplotr
docker stop $(docker container ls -q --filter name=isoplotr)
docker rm $(docker container ls -q -a --filter name=isoplotr)
docker images -qf dangling=true pvermees/isoplotr | xargs -r docker rmi
for p in $(seq 38001 38004)
do
docker run --restart unless-stopped -d --name isoplotr-${p} -p ${p}:80 pvermees/isoplotr
done

Now we can restart nginx and start isoplotr:

sudo systemctl restart nginx
isoplotr-start

crontab to keep IsoplotR up-to-date

Set up a cron job to update the Docker image at some time when you think it is not likely to be used (as a short period of downtime occurs when there is an update to be installed):

sudo -u wwwrunner crontab -e

Then add a line like this (to run at 03:17 local time):

17 3 * * * /usr/local/sbin/isoplotr-start | /usr/bin/logger

You can force an update yourself by running the script as the wwwrunner user:

sudo -u wwwrunner /usr/local/sbin/isoplotr-start

Maintenance

You can view the logs from the various processes mentioned here as follows:

Process command for accessing logs
cron (including the update script) journalctl -eu cron
systemD journalctl -e _PID=1
IsoplotRgui docker logs isoplotr
docker journalctl -eu docker but don't expect anything too helpful
nginx journalctl -eu nginx
nginx detail logs are written into the /var/log/nginx directory

journalctl has many interesting options; for example -r to see the most recent messages first, -k to see messages only from this boot, or -f to show messages as they come in. The -e option we have been using scrolls to the end of the log so that you are looking at the most recent entries immediately.

If you need to set a custom timeout (say, to 6.5 seconds in this example), change the docker run line in isoplotr-start like this:

docker run --restart unless-stopped -d --name isoplotr -p 3839:80 -e TIMEOUT=6.5 pvermees/