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Setting up your own online mirror with git

This method delivers the latest stable version of the app. Alternative methods include:

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

  2. Docker containers provide the most secure way to install an IsoplotR mirror.

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

Using the installer

With a Debian-based Linux distribution (such as Ubuntu) you can use our installer to set up IsoplotR quickly and easily.

sudo apt install isoplotr.deb

Now please skip to the Configuring IsoplotR section

By Hand

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

  • Ubuntu
  • nginx
  • R
  • git
  • crontab

You should usually use the installer method above, but if that does not work for you for some reason, here is how to do it manually.

Install nginx, R and git

If these packages are not installed on your system already, then you can add them with the following commands:

sudo apt-get install nginx git r-base r-base-dev

Create a user to run IsoplotR

It can be advantageous to have a non-human user running the applications such as IsoplotR that you are exposing over the web so as to limit any damage should one behave badly. For our purposes we will create one called wwwrunner:

sudo useradd -mr wwwrunner

Set up IsoplotRgui for this user

The version of IsoplotR and IsoplotRgui that gets run will be the version that our new user wwwrunner has installed.

Install IsoplotR for this user:

sudo -Hu wwwrunner sh -c "mkdir ~/R"
sudo -Hu wwwrunner sh -c "echo R_LIBS_USER=~/R > ~/.Renviron"
sudo -Hu wwwrunner Rscript -e "install.packages(pkgs='remotes',lib='~/R')"
sudo -Hu wwwrunner Rscript -e \
     "remotes::install_github(repo=c('pvermees/IsoplotR','pvermees/IsoplotRgui'),lib='~/R')"

Create a systemd service for IsoplotR

Copy the file isoplotr/etc/systemd/system/[email protected] into /etc/systemd/system/.

Copy all the files in isoplotr/usr/local/sbin/ into /usr/local/sbin/. isoplotrctl is your script for interacting with the isoplotr service; you can start it with:

sudo isoplotrctl start

Instead of start, you can also use the following verbs:

  • stop to stop the service
  • enable to ensure the service starts on boot
  • disable so that the service does not start on boot
  • status to see whether the service is up or down.

Expose IsoplotR with nginx

Copy the file isoplotr/etc/nginx/app.d/isoplotr.conf into /etc/nginx/app.d/ and isoplotr/etc/nginx/conf.d/isoplotr.conf into /etc/nginx/conf.d/. Now restart nginx with:

sudo systemctl nginx restart

and (providing that you also started the isoplotr service as described above) you should see isoplotr appear on [http://localhost/isoplotr/]. If not, see the Configuring IsoplotR section below.

Set up auto-updating

To ensure that IsoplotR is up-to-date, it is a good idea to set up auto-updating.

Copy the file isoplotr/etc/cron.weekly/isoplotr into /etc/cron.weekly/. This sets up the updating script to run every week (normally Sunday morning). You can run it yourself at any time with:

sudo /usr/local/sbin/updateIsoplotR.sh

Configuring IsoplotR

502 Bad Gateway

If you have run:

sudo systemctl restart nginx
sudo isoplotrctl start

and visited [http://localhost/isoplotr/] but only got a 502 Bad Gateway error, nginx is probably not including the configuration file /etc/nginx/app.d/isoplotr.conf. Check the file /etc/nginx/sites-available/default and look for the server block that contains the line listen 80 default_server;. If this block does not contain the line include /etc/nginx/app.d/*.conf; then you will have to add it yourself, so that the block looks something like this:

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

        # vvv ADDED THIS LINE HERE TO ENABLE ISOPLOTR
        include /etc/nginx/app.d/*.conf;

        root /var/www/html;

        # Add index.php to the list if you are using PHP
        index index.html index.htm index.nginx-debian.html;

        server_name _;

        location / {
                # First attempt to serve request as file, then
                # as directory, then fall back to displaying a 404.
                try_files $uri $uri/ =404;
        }
}

Now restart nginx with sudo systemctl restart nginx and see if visiting [http://localhost/isoplotr/] works now.

Horizontal Scaling

The installation described (either with the installer or manually) is fine for one user, but if many users are accessing the server they might find that they are sometimes waiting a long time for IsoplotR to respond, even when the server is only using a fraction of its power. This is because R is single-threaded, and so will only use one core.

You can mitigate this by running several services in parallel. The configureIsoplotR.sh script will configure this for you.

To upgrade to eight parallel services, you would run:

sudo configureIsoplotR.sh 8
sudo isoplotrctl start

You need to restart IsoplotR because configureIsoplotR.sh stops it.

If you find that IsoplotR is trying to use ports that are used for something else on your system, you can configure the port range it uses (it will use one port per parallel service).

To configure it to use ports 4001 to 4008, run:

sudo configureIsoplotR.sh 8 4001
sudo isoplotrctl start

(meaning 8 services starting with port 4001)

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 journalctl -eu isoplotr
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 ExecStart line in [email protected] like this:

ExecStart=/usr/bin/Rscript -e "IsoplotRgui::daemon(host='127.0.0.1', port=%i, timeout=6.5)"