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 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>
 
 ## Requirements
 
 - **Docker version 17.12.0-ce**
 
 ## Installation
 
 ### Set the Docker container external resources
 
 To avoid data loses when updating a container, use data storage on the host:
 
 ```
 $ mkdir /path/to/genocrunch/storage  # if users data storage location does not exist yet
 ```
 
 Also set a database to be used by the containers:
 
 ```
 $ 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
 ```
 
 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 
 ...
 ```
 
 Restart the PostgreSQL service:
 
 ```
 $ sudo /etc/init.d/postgresql restart
 ```
 
 ### Build the docker image
 
 Set the Dockerfile:
 
 ```
 $ cd /path/to/genocrunch
 $ cp Dockerfile.keep Dockerfile
 ```
 
 Edit these lines to set the app email address:
 
 ```
 #Dockerfile
 
 ...
 # config/config.yml
 ...
 RUN sed -i 's/info_links:.*$/info_links: [{name: "link_name", href: "link_url", target: "_blank"}]/g' config/config.yml
 RUN sed -i 's/user_confirmable:.*$/user_confirmable: false/g' config/config.yml
 
 # 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 line to fit the database name, user and password set previously:
+Edit these lines to fit the database name, user and password set previously:
 
 ```
 #Dockerfile
 
 ...
-# Set the database
+# config/database.yml
 ...
-RUN sed -i 's/username:.*$/username: genocrunch_user/g' config/database.yml
+RUN sed -i 's/^.*username:.*$/  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
+RUN sed -i 's/^.*password:.*$/  password: genocrunch_db_password/g' config/database.yml
 ...
 ```
 
 Finally, build the docker image:
 
 ```
 $ cd /path/to/genocrunch
 $ docker build --rm -t genocrunch .
 ```
 
 ### Run a docker container
 
 Run the docker container with the command below. Make sure to replace `/path/to/genocrunch/storage` with the appropriate path 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 the network.
 
 ```
 $ cd /path/to/genocrunch
 $ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch
 ```
 
-When used for the first time, initialize the database from within a docker container using `db/schema.rb` and `db/seeds.rb`:
+Complete the installation by initializing the database from within a docker container using `db/schema.rb` and `db/seeds.rb`:
 
 ```
 $ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch bash
 
 # Caution: this will overwrite the current database.
 # For updates, use migrations instead
 $ rails db:schema:load
 $ rails db:seeds
 $ exit
 ```