AnnotationHubServer3.0

the ruby version of AnnotationHubServer

How to install

Before attempting to install this server, consider whether the Dockerized version would better meet your needs.

System dependencies

Make sure you have mysql and sqlite3 (with headers) installed.

sudo apt-get install libsqlite3-dev mysql-server libmysqlclient15-dev

Installing Ruby and needed libraries

The simplest way is to use rbenv:

The following instructions are adapted from the rbenv page. It's worth reading this to understand how rbenv works.

Important note: Never use sudo when working with a ruby that has been installed by rbenv. rbenv installs everything in your home directory so you should never need to become root or fiddle with permissions.

1. Make sure you do not have rvm installed. which rvm should not return anything. If you do have it installed, refer to this page for instructions on removing it.

2. Check out rbenv into ~/.rbenv.

   ~~~ sh $ git clone https://github.com/sstephenson/rbenv.git ~/.rbenv ~~~

3. Add ~/.rbenv/bin to your $PATH for access to the rbenv command-line utility.

   ~~~ sh $ echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile ~~~

   Ubuntu Desktop note: Modify your ~/.bashrc instead of ~/.bash_profile.

   Zsh note: Modify your ~/.zshrc file instead of ~/.bash_profile.

4. Add rbenv init to your shell to enable shims and autocompletion.

   ~~~ sh $ echo 'eval "$(rbenv init -)"' >> ~/.bash_profile ~~~

   Same as in previous step, use ~/.bashrc on Ubuntu, or ~/.zshrc for Zsh.

5. Restart your shell so that PATH changes take effect. (Opening a new terminal tab will usually do it.) Now check if rbenv was set up:

   ~~~ sh $ type rbenv

   => "rbenv is a function"

   ~~~

6. Install ruby-build, which provides the rbenv install command that simplifies the process of installing new Ruby versions:

   git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build
   

7. Now you need to install ruby. Go to the Ruby Downloads Page to find out what the current stable version is. As of 3/30/2014 it is 2.1.1 so I will use that in further examples, but substitute the current stable version for 2.1.1 in what follows.

   To install this version of ruby in rbenv, type

   rbenv install 2.1.1
   

   Then, to make this the only version of ruby that you will use, type:

   rbenv global 2.1.1
   

   If you want to use different versions of ruby in different contexts, read the rbenv page for more information.

Installing Necessary Ruby Packages

Ruby packages are called gems and gem is the program used to install them.

The Gemfile is like a DESCRIPTION file and describes the package (gem) dependencies that are needed. this file is used by the bundler gem. So install bundler:

gem install bundler

And then tell bundler to read the Gemfile and install the packages specified there:

bundle install

Running the server

Get the sqlite3 database (annotationhub.sqlite3) from

http://gamay:9393/get_db

Copy it to the same directory where this README file lives.

Set the environment variable that tells us which type of database you are using:

export AHS_DATABASE_TYPE=sqlite

You could set it to mysql if you were using mysql.

Now cd to the same directory as this README and do:

shotgun app.rb

It will say:

== Shotgun/WEBrick on http://127.0.0.1:9393/
[2014-04-21 16:24:05] INFO  WEBrick 1.3.1
[2014-04-21 16:24:05] INFO  ruby 2.1.1 (2014-02-24) [x86_64-darwin13.0]
[2014-04-21 16:24:05] INFO  WEBrick::HTTPServer#start: pid=1156 port=9393

So you can open a web browser to http://127.0.0.1:9393/