3DBIONOTES-WS v3.12.1

Integrating molecular biology

3DBIONOTES-WS is a web application designed to automatically annotate biochemical and biomedical information onto structural models. Current sources of information include:

• post-translational modifications
• genomic variations associated to diseases
• short linear motifs,
• immune epitopes sites,
• disordered regions and
• domain families.

Setup

Setup Development

Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:

Note: To install rvm on Ubuntu, follow the instructions on the ubuntu rvm repository

$ rvm install ruby-3.3.1
$ gem install bundler:2.5.10
$ sudo apt install libmysqlclient-dev # Debian/Ubuntu
$ bundle install
$ cp config/database.example.yml config/database.yml
$ cp config/secrets.example.yml config/secrets.yml
$ bundle exec rake db:migrate RAILS_ENV=development
$ bundle exec rails server

Setup Developent on macOS

Before you start your setup, make sure you have homebrew, ruby, rvm and python2 installed. Use rvm or rbenv to select the Ruby version specified in Gemfile and then run:

$ rvm install ruby-3.3.1
$ gem install bundler:2.2.15
$ brew install mysql
$ gem install bundler:2.0.0.pre.3

In the Gemfile, remove Gem specs for mini_racer and libv8 and the dependency for mini_racer

$ bundle _2.0.0.pre.3_ install
$ cp config/database.example.yml config/database.yml
$ cp config/secrets.example.yml config/secrets.yml
$ bundle exec rake db:migrate RAILS_ENV=development
$ bundle exec rails server

Setup docker-compose

1. Create .env file from .env.sample
2. Uncomment and fill the mandatory environment variables in the .env file, w: APP_BASE_PATH, APP_DATABASES_PATH, BLAST_BIN,BLAST_DATABASE and DB_EXT_DBS. Docker compose won't launch the containers otherwise or if they are empty. The value needed is a path to bind in your system.
3. (Optional) Adapt the reamining environment, such as ports and database credentials
4. Start docker containers with following command

docker compose --env-file .env -f docker-compose.development.yml up -d

Re-build container:

docker compose --env-file .env -f docker-compose.development.yml up -d --build

Stop all containers:

docker compose -f docker-compose.development.yml down

Setup Viewer

If you want to set up the React protein viewer as well, open up a separate terminal tab (while the Ruby app is running!) and run:

$ cd app/assets/javascripts/3dbio_viewer/
$ yarn install
$ yarn start

Then go to localhost:3001 and you'll see the viewer!

Setup Production

Add Passenger setup to /etc/apache2/apache2.conf:

LoadModule passenger_module /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12/buildout/apache2/mod_passenger.so
   <IfModule mod_passenger.c>
     PassengerRoot /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12
     PassengerDefaultRuby /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/wrappers/ruby
     PassengerMaxPoolSize 64
     PassengerMinInstances 32
     PassengerPoolIdleTime 60
   </IfModule>

The site configuration file (/etc/apache2/sites-enabled/bionotes) for Apache should like this:

<VirtualHost *:80>
   ServerName XXX.cnb.csic.es
   PassengerRoot /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/gems/passenger-5.1.12
   PassengerRuby /services/bionotes/.rvm/gems/ruby-2.4.1@bionotes/wrappers/ruby
   DocumentRoot /services/bionotes/apps/bionotes/public
   RailsEnv production
   <Directory /services/bionotes/apps/bionotes/public>
      # This relaxes Apache security settings.
      AllowOverride all
      # MultiViews must be turned off.
      Options -MultiViews
      # Uncomment this if you're on Apache >= 2.4:
      #Require all granted
   </Directory>
</VirtualHost>

And finally, run:

$ rvm install ruby-2.4.1
$ passenger-install-apache2-module --auto
$ sudo a2ensite bionotes
$ sudo ln -s /services/bionotes/apps/node/bin/node /usr/local/bin/node
$ RAILS_ENV=production bundle exec rake assets:precompile
$ sudo /etc/init.d/apache2 restart

To perform an app restart after a change, just run:

$ touch tmp/restart.txt

Deploy

Depending on the environment some changes should be made in these files:

• config/environments/development.rb (config hostnames)
• config/settings.yml (base url)
• app/assets/javascripts/webserver/webserver_init.js (ga4 code)

Alternatively, for the webserver_init.js file, a script could be executed:

$ bash scripts/deploy/set_ga_code.sh --environment [development|production]

Delayed Jobs

The network sections run a set of jobs in the background on the server. To work properly, a delayed job daemon needs to be running on the server:

$ RAILS_ENV=production bin/delayed_job -n 6 restart

Other dependencies

• ngl

  • Repository: https://github.com/arose/ngl

• jsmol

  • Path: app/assets/javascripts/jsmol

Copyright (c) 2020, Biocomputing Unit, CNB-CSIC