Installing and Running Aquarium
We recommend that labs doing protocol development run at least two instances: the first, a nursery server that is shared within the lab for the purposes of trying out protocols under development, while the second is the production server that controls the lab. We use this arrangement in the Klavins lab to run the UW BIOFAB so that protocols can be evaluated without messing up the actual lab inventory. In addition, each protocol developer should run a local instance, which can be done easily with Docker.
Table of Contents
- Installing and Running Aquarium
Choosing your Approach
Manual Installation: If your goal is to run Aquarium in production mode with many users, you should install and run Aquarium manually. This requires first installing Ruby, Rails, MySQL, and, depending on the deployment, a web server. The UW BIOFAB, for example, runs Aquarium on an Amazon Web Services EC2 instance using the web server nginx and the MySQL database running on a separate RDBMS instance.
We discuss some of the considerations for running Aquarium below, but your deployment may require fine-tuning beyond what we describe.
Jump to manual installation instructions.
Docker Installation: If your goal is instead to run Aquarium on your laptop to evaluate it, develop new code, or serve a small lab, we have provided a Docker configuration script that runs Aquarium in the Rails development mode.
Jump to docker installation instructions.
We strongly encourage protocol developers to use the Docker version in development mode, because it eliminates several of the configuration details needed for production. Once a protocol runs well on a local instance, you can port it to your production instance using import on the developer tab.
We understand that it might seem simpler to set up a single instance of Aquarium and use it as the production server and for protocol development. However, protocol testing should not be done on a production server, because protocol errors can affect system performance, and protocols that create database entries can pollute your production database.
Manual Installation Instructions
To manually install Aquarium in a production environment:
Ensure you have a Unix-like environment on your machine and have installed
Also, make sure that you have a MySQL server installed.
When installing Aquarium on AWS or another cloud service, you should use RDBMS or the database services available there.
Get the Aquarium source code by either downloading the latest release, or cloning the repository.
The latest release is available as either a zip or tar.gz file. Download the file that you are able to un-compress. For instance, on a Unix machine, download the tar.gz file, and use the command
tar xzf aquarium-v2.201.tar.gz
Replacing the file name with the name for the latest release.
Alternatively, clone the repository and checkout the latest tagged commit
git clone https://github.com/klavinslab/aquarium.git cd aquarium latest=`git describe --tags` git checkout $latest
Note: this version may be more recent than the latest release.
Configure Aquarium by first creating the
cd aquarium/config/initializers cp aquarium_template.notrb aquarium.rb
and then editing
aquarium.rbto set the URLs and email address.
Configure the Aquarium database settings. First, create the
cd .. # aquarium/config cp database_template.yml database.yml
You should change the production mode configuration to point to your database server. And, in this case, you don’t need to worry about the remainder of the
Otherwise, the default settings for the development and test modes should be sufficient, unless you want to use a full database in development mode. Regardless, the test mode for running Aquarium system tests should use the
Install the Ruby gems required by Aquarium with
gem install bundler bundle install
Note: if the MySQL database is not installed or not properly installed/configured, you may get errors during this step.
npm install -g bower bower install
Initialize the database with
RAILS_ENV=production rake db:schema:load
You can also set
rehearsein place of
production. Any mode that is specified in
For the production server, precompile the assets:
RAILS_ENV=production bundle exec rake assets:precompile
To start Aquarium, run
RAILS_ENV=production rails s
and then go do
http://localhost:3000/to find the login page.
Also, start the Krill server
rails runner "Krill::Server.new.run(3500)"
Docker Installation Instructions
These instructions are for setting up a local Aquarium and are not meant for production instances.
To run Aquarium with Docker:
Install Docker on your computer.
Note that our setup scripts are written for a Unix™ environment. They will work on OSX, Linux, or inside the Docker Toolbox VM on Windows. To run Aquarium on Windows your system either needs to meet the requirements of Docker for Windows, or you have to use the older Docker Toolbox.
Either get the latest release latest release and uncompress the file, or clone the Aquarium repository
git clone email@example.com:klavinslab/aquarium.git
If using Docker Toolbox for Windows
git clone firstname.lastname@example.org:klavinslab/aquarium.git --config core.autocrlf=input
development-setup.shscript to setup the development environment
cd aquarium ./development-setup.sh
If using Docker Toolbox for Windows
cd aquarium ./development-setup.sh windows
This script moves default development configuration files into the correct place. You only need to run it once.
To build the docker images, run the command
For protocol development, this should only be necessary before running Aquarium for the first time after cloning or pulling the repository. Though, run this step again if you have trouble and changes may have been made.
To start aquarium, run the command
which starts the services for Aquarium. The first run initializes the database, and will take longer than subsequent runs.
Once all of the services for Aquarium have started, visit
localhost:3000with the Chrome browser and you will find the Aquarium login page. If running aquarium inside the docker toolbox VM, the address will be instead be
192.168.99.100:3000. The default database has a user login
To halt the Aquarium services, first type
ctrl-cin the terminal to stop the running containers, then remove the containers by running
Some configuration notes:
When running Aquarium, you may notice a prominent name Your Lab in the upper left-hand corner. If this bugs you, you can change it to something you prefer by replacing the string at the end of the first line in
config/initializers/aquarium.rb, which is currently
Bioturk::Application.config.instance_name = 'Your Lab'
You might change it to
'George'. The choice is yours.
The Docker configuration stores the database files in
The database is initialized with the contents of
docker/mysql_init/dump.sql, but changes you make will persist between runs.
You can use a different database database dump by renaming it to this file, removing the contents of the
docker/dbdirectory and restarting Aquarium.
Uploaded files currently are not compatible with a docker installation. This feature is coming soon to the dockerized version, but in the mean time: if you need to locally test workflows that upload files, the manual installation will be necessary.