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readme.rst

Yabi

About

Yabi is a 3-tier application stack to provide users with an intuitive, easy to use, abstraction of compute and data environments. Developed at the Centre for Comparative Genomics (https://ccg.murdoch.edu.au/), Yabi has been deployed across a diverse set of scientific disciplines and high performance computing environments.

Yabi has a few key features:

  • simplified web based access to High Performance Computing
  • easy tool addition and maintenance
  • handling of disparate compute and storage resouces ie. PBSPro, SGE, Torque, Slurm, SSH, SFTP, Amazon S3, Openstack Swift
  • easy and powerful workflow creation environment

More docs at Read the Docs (https://yabi.readthedocs.org/).

Contact

Hosted on GitHub:

https://github.com/muccg/yabi/

Documentation on Read the Docs:

https://yabi.readthedocs.org/

Twitter:

http://twitter.com/#!/yabiproject

YouTube:

https://www.youtube.com/playlist?list=PLA7CAEC7DAA530AFA

Email:

yabi@ccg.murdoch.edu.au

For developers

We do our development using Docker containers. See: https://www.docker.com/. You will have to set up Docker on your development machine.

Other development dependencies are Python 2 and virtualenv (https://virtualenv.pypa.io/en/latest/).

All the development tasks can be done by using the develop.sh shell script in this directory. Please run it without any arguments for help on its usage.

Some typical usages are:

  • ./develop.sh dev_rebuild
    You will need to run this the first time after you clone our repo to build the docker containers. You will also need to re-run it if you would like to rebuld the docker containers, for example when your python dependencies change.
  • ./develop.sh dev
    To start up all the docker containers needed for dev. You can access the Django Yabi application on http://localhost:8000 (replace localhost with $ boot2docker ip if using boot2docker) after this. You can login with one of the default users demo/demo or admin/admin.
  • ./develop.sh runtests
    Starts up all the docker containers and runs all our tests against them.
  • ./develop.sh pylint
    Lint your python code.
  • ./develop.sh jslint
    Lint your javascript code.

Note: Our docker containers are coordinated using docker-compose (https://docs.docker.com/compose/) but docker-compose will be installed into a virtualenv environment automatically by the ./develop.sh script for you.

Contributing

  1. Fork next_release branch
  2. Make changes on a feature branch
  3. Submit pull request

Citation

Hunter AA, Macgregor AB, Szabo TO, Wellington CA and Bellgard MI, Yabi: An online research environment for Grid, High Performance and Cloud computing, Source Code for Biology and Medicine 2012, 7:1 doi:10.1186/1751-0473-7-1 Published: 15 February 2012 Source Code for Biology and Medicine (http://www.scfbm.org/content/7/1/1/abstract)