BarKeeper

A versatile web framework to assemble, analyze and manage DNA barcode data and metadata.

• Example implementation: barkeeper.uni-muenster.de (credentials: [email protected] - barkeeper2022)

Using BarKeeper for your own project

You can set up your own project with BarKeeper Web Framework easily by running it via Docker. If you don't know what Docker is, read their excellent Get Started with Docker guide.

For testing purposes BarKeeper can be set up on any server or personal computer with an OS capable of running Docker. However, for running BarKeeper in a production environment we strongly recommend setting up a server with a current version of Ubuntu and sufficient hardware to handle your project's needs. Remember that this needs to be done only once per project. Every other member will be able to use BarKeeper simply from their web browser without the need of installing anything else.

Prerequisites

Here's what you need to prepare before you can start the setup process:

• Make sure that you have a stable internet connection during all steps of the setup process.
• Have a server or Desktop computer running any OS capable of supporting Docker. Setup was tested on machines running Ubuntu 16.04 up to 22.04 and Windows 10 with WSL enabled.
  • Windows: We recommend running all commands to install BarKeeper from within a WSL Ubuntu instance after installing Docker Desktop via the executable file provided by Docker.
  • Ubuntu versions: Older versions of Ubuntu will likely work as well but are not getting security updates any longer (this is also true for Ubuntu 16.04 by now) so using those cannot be recommended in a production environment.
• You will also need a user with superuser or administrative rights during the installation process.
• It is highly recommended that you establish suitable server security measures like a properly configured firewall in case you want to make BarKeeper accessible from the internet.
• Install Docker Engine or Desktop (choose the appropriate tutorial for your OS here). The setup was tested with Docker version 18.06 and higher. Older versions may work but this cannot be guaranteed.
• Install Docker Compose (for newer versions of Docker this is already a part of the Docker installation). You can find detailed instructions here. The setup was tested with Docker-Compose version 1.27 and higher. Older versions may work but this cannot be guaranteed.
• Clone the code from this repository to a suitable location on your computer or server via Git (you may need to download and install Git first).
• Make sure the ports used by redis and postgres are not already in use on your machine (redis: 6379, Postgres: 5432).
• If you want to run mislabel analyses on the sequences stored in your database on a remote server (SSH address can be specified in .env file) make sure that the SATIVA files are available and the alignment tool MAFFT is installed there. More information about SATIVA can be found here.
• Optional: You can install GNU Make for an easier setup and running BarKeeper with simple commands.

Setup

• Find the file .env-example and copy it to a new file .env in the main directory of the repository you just cloned.

• Modify the .env file to your project's needs. Values that you need to change are described as such in the file. The same goes for variables that generally should not (or don't need to) be changed. You do not need to add values for SECRET_KEY_BASE and DEVISE_KEY yet! If you want the app to run on a port different to the standard port 80, please specify your desired port number in the environment variable PORT. The value of the variable PUMA_PORT should generally not be changed.

  • After setting up all other environment variables and saving the file, generate secret keys for Rails and Devise by running make secret two times and copying the generated random keys from your command line. Add the first key as the value for SECRET_KEY_BASE and the second as the value of DEVISE_KEY in your .env file and save it.
    • The first time you run the make secret command, this will install all dependencies inside the app docker container. This can take some time! The following invocation should run much quicker then.
    • If you cannot or do not want to use make, you can run the command docker-compose run app rails secret instead.

• Now you can install the whole app by running make install.

  • If you can not or do not want to use make, run these commands instead in this order:
    • docker-compose run app rails db:reset
    • docker-compose run app rails assets:precompile
    • docker-compose up -d

• You should be able to see the about page of your project's new app on your domain now. Even if you did not specify any domain, you can always find BarKeeper running on "localhost".

  • HTTPS is not enabled yet. If you want to configure this, you will have to change the nginx.conf file manually and install a certificate. You can find more information here or contact the developers of BarKeeper for help on this.

• Use the admin credentials you added to the .env file to initially log in and create new records for your project.

  • You can start by going to the Admin area > Home configuration page and change the About page background and add a description of your project.

• You are done! Now you and your team can use the new app and start uploading data!

• To stop and restart the app use the commands make stop followed by make start or just make restart.

  • Instead you can run docker-compose down and docker-compose up -d

• To remove unused BarKeeper containers created on your system use make remove.

  • Instead you can use docker-compose rm -s -v -f

Further notes

• BarKeeper uses location data maps with map tiles from the Open Street Map Foundation. Please check if your implementation might need to use a different provider of map tiles as per their Tile Usage Policy to avoid being blocked from their services. You can change the map tile layer in the app/assets/individuals.js file.

License

Copyright (C) 2022 Kai Müller [email protected], Sarah Wiechers [email protected]

BarKeeper is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BarKeeper is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with BarKeeper. If not, see http://www.gnu.org/licenses/.