Railroadtracks
Railroadtracks is a Python package to handle connected computation steps for DNA and RNA Seq.
| Branch | |
|---|---|
| Master |  |
| version_0.4.x |  |
| version_0.3.x |  |
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.
