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