Goal

Simple ruby library for accessing myExperiment via REST


Introduction

The myExperiment workflow repository (www.myexperiment.org) provides a REST API to access its information. This is a simple library to access some of the workflow and user data available in myExperiment and make them available as ruby objects. It provides a subset of what is available, particularly what was needed from my other projects. However, it is easy to extend so contact me if you want more information exposed.

References

  1. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic acids research, Vol. 38 (suppl 2): W677-W682, 2010.
  2.  http://www.myexperiment.org

Requirements

The tool is implemented in Ruby, so a Ruby development environment needs to be available. Native packages of libxml, libopenssl and zlib may be required. Please use your favorite package manager to install them (an apt-get example is given). Note that some of the following native packages might already be installed in your system. For Debian-based systems, use this command:

$ sudo apt-get install ruby rubygems gcc build-essential libopenssl-ruby ruby1.8-dev libxml2-dev

To install the myexperiment-rest library type the following command:

$ sudo gem install myexperiment-rest

Testing

Test that it is correctly installed by typing:

$ get_workflow_data.rb

Note that in some systems the executable will not be automatically in the path. Run:

$ gem environment

and add the value of EXECUTABLE DIRECTORY to your PATH.

Contact

  • Kostas Karasavvas -- kostas (dot) karasavvas (at) nbic (dot) nl
  • Marco Roos -- m (dot) roos1 (at) uva (dot) nl

Back to parent project elabfactory.