Table of Contents

Requirements

  • Linux or Mac system with the following programs available on the command line: sed, wget and gunzip. These programs are available in most Linix distributions.
  • Ruby programming language (version 1.8.X), the RubyGems packaging system and Rake (Ruby 'make') - in Ubuntu: sudo apt-get install ruby ruby-dev rubygems and gem install rake.
  • One of the following database management systems:

Downloading

miRmaid can be downloaded from the GitHub repository manually

wget http://github.com/andersjacobsen/mirmaid/zipball/master
tar zxf andersjacobsen-mirmaid-*.tar.gz

or by cloning the source code using the Git revision control system (requires that you have installed Git on your system already)

git clone git://github.com/andersjacobsen/mirmaid.git my_mirmaid_dir

Installing

Navigate to your MirMaid directory and copy/rename the following two files:

cd my_mirmaid_dir
cp config/mirmaid_config.yml.example config/mirmaid_config.yml
cp config/database.yml.example config/database.yml

These two files configures the database (database.yml, read more) and the MirMaid system (mirmaid_config.yml, read more). You can leave these two files unchanged. The default configuration will use the Sqlite database system (a simple database recommended for situations with few concurrent users) and fetch the latest miRBase data release from the miRBase FTP site.

Next, we need to install some dependencies (maybe you need to run the command with 'sudo …' if you are installing gems in a system directory):

gem install json ferret
gem install rack --version  '~> 1.0.1'
gem install acts_as_ferret --version '= 0.4.4'

Another dependency is the Sqlite3 database system (that is if you use the default MirMaid configuration). If you use Mac OSX >= 10.5 you are in luck, Sqlite3 should already be installed in your system. If you use Linux, it is easy to install Sqlite3 using your package manager. In Ubuntu you can run the following command:

sudo apt-get install sqlite3 libsqlite3-dev libsqlite3-ruby

Finally, in Ubuntu you might need the following package for the REST test suite to work:

apt-get install libopenssl-ruby 

Run the MirMaid installation script. This process takes about 15 minutes (depending on your system and configuration). The installer requires wget to be in your path. On Mac OSX it is not installed by default, install wget with MacPorts

sudo port install wget

Then you are ready to load your database with miRbase data.

rake mirmaid:load

That's it! You should check that the last part of the ouput from the MirMaid installation script reports 0 failures/errors.

<...>
Loaded suite /home/andersbj/myruby/gems/gems/rake-0.8.7/lib/rake/rake_test_loader
Started
.....................
Finished in 0.34903 seconds.
 
21 tests, 33 assertions, 0 failures, 0 errors
<...>

If you already have a miRMaid database configured and you for example want to update this database with the newest version of miRBase, then you should use another command that will start out by 'dropping' your database:

rake mirmaid:reset

You can now proceed to install one of the optional plugins or read more about how you can use MirMaid from your own programs in the API tutorial. Another possibility is to run the web-interface locally on your own machine, with the command:

script/server -e production
Then point your webbrowser to http://localhost:3000/

You can always check that your installation is healthy by running the test suite:

rake mirmaid:test:all

 
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install_quick.txt · Last modified: 2010/03/01 20:14 by morten.lindow