Railroadtracks is a Python package to handle connected computation steps for DNA and RNA Seq.
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README.md

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Railroadtracks

Railroadtracks is a Python package to handle connected computation steps for DNA and RNA Seq.

PyPI version

Branch
Master Build Status
version_0.4.x Build Status
version_0.3.x Build Status

Installation

The documentation should be consulted for information about the requirements and the installation process.

While we are working on a link to a build of the documentation, the Sphinx source for it are be consulted: doc/installation.rst.

Released versiond are available on Pypi. Installing the latest release is as easy as:

pip install railroadtracks

The use the development version, the master branch can be installed with

pip install https://github.com/Novartis/railroadtracks/archive/master.zip

A Docker container is also availale (lgautier/railroadtracks).

# pull the Docker images from docker.io
docker pull lgautier/railroadtracks 
# Run an ipython notebook server from the container
docker run -it -p 8888:8888 -w /usr/local/packages/railroadtracks/doc/notebooks lgautier/railroadtracks ipython notebook --ip=0.0.0.0 --no-browser

A browser running on the same machine as the container can then be pointed to: http://localhost:8888

If on a non-Linux system using boot2docker, you may have to point your browser to the IP mapped to the VM docker is running in. The IP can be obtained with:

boot2docker ip

Documentation

Sphinx documentation is included in the source tree. An HTML build of the documentation is available at http://pythonhosted.org/railroadtracks/.

The tutorial http://pythonhosted.org/railroadtracks/tutorial.html is a genuine notebook rendered into the Sphinx document. The notebook and an HTML render of it are available, and running ipython notebook through the container (see above) provides a complete environment to go through the tutorial.