szitenberg/reprophylo repository overview

⁠ReproPhylo: Reproducible Phylogenetics

ReproPhylo is a reproducible phylogenetics pipeline written in python and making use of BioPython and other open tools. This is an implementation in IPython notebook

⁠Galaxy version⁠

⁠Dockerfile⁠

⁠Licence

ReproPhylo is in the public domain under a CC0 licence⁠. This is a 'no copyright' licence and you are free to use, modify and repurpose any part of our work as you see fit. Some of the dependencies have more constricting licences. See the documentation⁠ for details.

⁠Documentation

Docs and guides are available in a public Google Doc⁠, and you are encouraged to edit, extend and improve these docs if you wish.

⁠Contributions

We welcome your additions and improvements, just fork the repository on GitHub⁠ and then send a pull request.

⁠Installation

For Windows and Mac go here⁠
Otherwise:
Install Docker⁠

⁠Starting-up

The shell script startRP can be downloaded from here⁠ and run as follows:

usage:

$ sh ./startRP /path/to/your/dir

It will start up the default web browser at the IPython notebook login page. The password is 'password'. More on this script in the manual⁠.

Only files in the path you have specified will be accessible from within the container.

⁠Cleaning up

The following script will stop the container and delete it. Files you have written in the session will remain in the path you have specified upon start-up.

$ sudo docker rm -f rpnotebook