Ruby on Rails 5 with JDBC(MySQL)環境を作ります。
前提条件として、MySQL Serverをローカルで稼働しており、必要なデータベース(jruby_schema、jruby_schema_development)は作成しているものとします。
また今回は、JDBCはJARファイルを使います。

1. Gitのインストール

[Linux]

$ yum -y install git

*rootユーザーもしくはsudoで

[Mac]

Xcodeをインストール
Homebrewをインストール

2. rbenvのインストール(anyenvでも可)

[Linux]

$ git clone https://github.com/sstephenson/rbenv.git ~/.rbenv
$ echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile
$ echo 'eval "$(rbenv init -)"' >> ~/.bash_profile

[Mac]

$ brew install rbenv
$ brew install ruby-build

参考リンク

rbenv を使って ruby をインストールする(CentOS編)
MacにrbenvでRubyを簡単にインストールしてみる

2. jrubyのインストール、設定

$ rbenv install --list
  (中略)
  jruby-9.1.3.0
  jruby-9.1.4.0
  jruby-9.1.5.0
  maglev-1.0.0
  maglev-1.1.0-dev
  maglev-2.0.0-dev
  (中略)
$ rbenv install jruby-9.1.5.0
$ rbenv rehash
$ rbenv versions
* system
  jruby-9.1.5.0
$ rbenv global jruby-9.1.5.0

3. Gemのインストール

$ gem install bundler rails jdbc-mysql

4. Railsアプリの初期化

$ rbenv exec rails new test-app -d jdbcmysql
$ cd test-app

5. Gemfileの変更(jdbcのRails5対応)

test-app/Gemfile

# 下記をコメントアウト
# gem 'activerecord-jdbc-adapter'
# 下記を追記
gem 'activerecord-jdbc-adapter', github: "jruby/activerecord-jdbc-adapter",
                                 branch: "rails-5"
# ただし、jdbc-mysqlは今回使わない
# gem 'jdbc-mysql', github: 'jruby/activerecord-jdbc-adapter',
#                   branch: 'rails-5'

6. Gemfileにjbunlderの追加

test-app/Gemfile

# 以下を追記
# Use jbundler https://github.com/mkristian/jbundler
gem 'jbundler', '>= 0.9.3'

7. Gemfileにjar-dependenciesの追加

test-app/Gemfile

# 下記を追記
# Use jar-dependencies https://github.com/mkristian/jar-dependencies
gem 'jar-dependencies', '>= 0.3.5'

8. Gemfileにdevelopment環境向けgemを追記

test-app/Gemfile

# 下記を追記
group :development, :test do
  # Call 'byebug' anywhere in the code to stop execution and get a debugger console
  gem 'byebug', platform: :mri
end

group :development do
  # Access an IRB console on exception pages or by using <%= console %> anywhere in the code.
  gem 'web-console'
  gem 'listen', '~> 3.0.5'
  # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
  gem 'spring'
  gem 'spring-watcher-listen', '~> 2.0.0'
end

9. Jarfileを追加

test-app/Jarfile

# 以下を記述したJarfileを保存
jar 'mysql:mysql-connector-java', '5.1.39'
# 6.0.Xだとエラーになる

10. bundlerでGemを再インストール

$ bundle install

11. jbundlerでJAR(MySQL JDBC)をインストール

$ jbundle install

12. config/boot.rbの修正

test-app/config/boot.rb(変更前)

ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)

require 'bundler/setup' # Set up gems listed in the Gemfile.

test-app/config/boot.rb(変更後)

ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
#追記開始
require 'jbundler' # Use jbundler for some JARs.
#追記終わり
require 'bundler/setup' # Set up gems listed in the Gemfile.

12. config/database.yamlの修正

test-app/config/database.yaml

# MySQL. Versions 5.0 and up are supported.
#
# Install the MySQL driver:
#   gem install activerecord-jdbcmysql-adapter
#
# Configure Using Gemfile
# gem 'activerecord-jdbcmysql-adapter'
#
# And be sure to use new-style password hashing:
#   http://dev.mysql.com/doc/refman/5.7/en/old-client.html
#
default: &default
  adapter: jdbc
  jndi: jdbc/jruby
  username: root
  password: password
  host: localhost
  encoding: utf8
  reconnect: true
  pool: 8
  driver: com.mysql.jdbc.Driver
  url: jdbc:mysql://127.0.0.1:3306/jruby_schema
  database: jruby_schema
  properties:
    autoReconnect: true
    autoReconnectForPools: true
    defaultFetchSize: 1000
    requireSSL: false
    useCursorFetch: true
    useSSL: false
    useUnicode: true

development:
  <<: *default
  database: jruby_schema_development

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  <<: *default
  database: jruby_schema_test

# As with config/secrets.yml, you never want to store sensitive information,
# like your database password, in your source code. If your source code is
# ever seen by anyone, they now have access to your database.
#
# Instead, provide the password as a unix environment variable when you boot
# the app. Read http://guides.rubyonrails.org/configuring.html#configuring-a-database
# for a full rundown on how to provide these environment variables in a
# production deployment.
#
# On Heroku and other platform providers, you may have a full connection URL
# available as an environment variable. For example:
#
#   DATABASE_URL="mysql://myuser:mypass@localhost/somedatabase"
#
# You can use this database configuration with:
#
#   production:
#     url: <%= ENV['DATABASE_URL'] %>
#
production:
  <<: *default

13. Railsアプリをスタート

$ jruby -S bin/rails s