Genocrunch in Docker

A Dockerfile to run Genocrunch web application on Docker.

Resources

• Git clone URL: https://c4science.ch/source/genocrunch_docker.git
• Documentation: https://c4science.ch/source/genocrunch_docker
• Genocrunch documentation: https://c4science.ch/source/genocrunch-2.1
• Genocrunch official web server: https://genocrunch.epfl.ch

Rights

• Copyright: All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Laboratory of Intestinal Immunology, 2018
• License: MIT (See LICENSE.txt for details)
• Author: A Rapin

Requirements

• Docker version 17.12.0-ce

Installation (on Debian linux)

Note: you may have to use sudo with docker commands if docker is not configured to be used as a non-root user.

Set the Docker container external resources

The Genocrunch web application will need to store some data files and to use a database. To avoid data loses when updating a container, you can set both data storage location and database on the host (as opposed to set it up on the docker container itself).

First, create a new data storage directory on the host side. This directory will be used by the Genocrunch web app running on the docker container:

$ mkdir /path/to/genocrunch/storage

Also create a PostgreSQL database on the host side. This database will be used by the Genocrunch web app running on the docker container:

$ sudo apt-get install postgresql postgresql-contrib
$ sudo su postgres
$ psql
postgres=# create role genocrunch_user with login password 'genocrunch_db_password';
postgres=# create database genocrunch owner genocrunch_user;
postgres=# \q
$ exit

Then, allow the docker container to be listened from the database by modifying the /etc/postgresql/9.?/main/postgresql.conf file as following:

#/etc/postgresql/9.?/main/postgresql.conf 
...
listen_addresses = '*'
...

Also add the following line to /etc/postgresql/9.?/main/pg_hba.conf:

#/etc/postgresql/9.?/main/pg_hba.conf 
...
host    all             all             0.0.0.0/0               md5 
...

Finally, restart the PostgreSQL service:

$ sudo /etc/init.d/postgresql restart

Build the docker image

First, download the Dockerfile from its git repository:

$ git clone https://c4science.ch/source/genocrunch_docker.git

Before building a docker image using the Dockerfile, you may want to edit the Dockerfile in order to customize the installation of the Genocrunch web app. For this, open genocrunch_docker/Dockerfile with your favorite editor and follow the following instructions:

Edit this line to define the CRAN mirror from which to download R packages:

#Dockerfile

...
RUN echo "options(repos=structure(c(CRAN='https://stat.ethz.ch/CRAN')))" >> .Rprofile
...

Edit this line to define any custom link to be included in the info menu of the Genocrunch web app topbar:

#Dockerfile

...
# config/config.yml
...
RUN sed -i 's/info_links:.*$/info_links: [{name: "link_name", href: "link_url", target: "_blank"}]/g' config/config.yml
...

Edit this line to define whether new users will be asked to confirm their email address via a confirmation link or not:

#Dockerfile

...
# config/config.yml
...
RUN sed -i 's/user_confirmable:.*$/user_confirmable: false/g' config/config.yml
...

Edit these lines to set the email address to be used by the web app:

#Dockerfile

...
# config/initializers/devise.rb
...
RUN sed -i 's/config.mailer_sender =.*$/config.mailer_sender = "app_email@gmail.com"/g' config/initializers/devise.rb

# config/environments/development.rb
...
RUN sed -i 's/config.action_mailer.default_url_options =.*$/config.action_mailer.default_url_options = {:host => "localhost:3000"}/g' config/environments/development.rb
RUN sed -i 's/:address =>.*$/:address => "smtp.gmail.com",/g' config/environments/development.rb
RUN sed -i 's/:port =>.*$/:port => 587,/g' config/environments/development.rb
RUN sed -i 's/:domain =>.*$/:domain => "mail.google.com",/g' config/environments/development.rb
RUN sed -i 's/:user_name =>.*$/:user_name => "app_email@gmail.com",/g' config/environments/development.rb
RUN sed -i 's/:password =>.*$/:password => "app_email_password",/g' config/environments/development.rb
RUN sed -i 's/:authentication =>.*$/:authentication => :plain,/g' config/environments/development.rb
RUN sed -i 's/:enable_starttls_auto =>.*$/:enable_starttls_auto => true/g' config/environments/development.rb
...

Edit these lines to fit the database name, user and password set previously:

#Dockerfile

...
# config/database.yml
...
RUN sed -i 's/^.*username:.*$/  username: genocrunch_user/g' config/database.yml
RUN sed -i 's/database:.*$/database: genocrunch/g' config/database.yml
RUN sed -i 's/^.*password:.*$/  password: genocrunch_db_password/g' config/database.yml
...

Finally, build the docker image:

$ docker build --rm -t genocrunch .

Database initialization

Complete the installation of the Genocrunch web app by initializing its database from within a docker container using rails schema (db/schema.rb) and seeds (db/seeds.rb). Caution: this will overwrite the database and should be applied only for initialization/re-initialization, not updates. For updates, use migrations or SQL queries.

$ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch bash
$ rails db:schema:load

# To change default guest and admin passwords, emails and storage quotas, edit the `User.create` query in the db/seeds.rb file with nano:
$ nano db/seeds.rb

# Finally, seed the database:
$ rails db:seed
$ exit

Run a docker container

Run a docker container using the command below. Make sure to replace /path/to/genocrunch/storage with the appropriate path (see the Set the Docker container external resources section above) and replace host.ip.address by the host ip address. This will automatically start the Genocrunch web server which will be accessible in a web browser at http://localhost:3000 on the host and host.ip.address:3000 on your network.

$ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch