A Galaxy instance with ReproPhylo tools
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galaxy-dist
INSTALL.sh
README.md

README.md

ReproPhyloGalaxy

A Galaxy instance with ReproPhylo tools

ReproPhylo: Reproducible Phylogenetics

ReproPhylo is a reproducible phylogenetics pipeline written in python and making use of BioPython and other open tools. This is a Galaxy instance with ReproPhylo tools.

Galaxy version:

Galaxy was cloned and updated to 'stabe' on 27 Nov 2014 using
hg clone https://bitbucket.org/galaxy/galaxy-dist/
cd galaxy-dist && hg update stable

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. See the documentation for licences of dependencies.

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. The manual includes a Galaxy tutorial.

Contributions

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

Installation on a Ubuntu 14.10 machine

(for the Galaxy instance including the ReproPhylo tools and the dependencies)

  1. clone or downlad and extract this repository
  2. cd ReproPhyloGalaxy
  3. ./INSTALL.sh

You will be asked for sudo password

Note: After the installation is done the repository directory can be removed

Running Galaxy

  1. cd ~/galaxy-dist
  2. sudo sh run.sh
  3. In a web browser, go to https://localhost:8080

The first start-up takes a while because galaxy will fetch online eggs and will conduct tests. Subsequent start-ups are quick.

Note: If you have troubles shutting down galaxy with ctrl+c, restart the machine and use sudo sh run.sh --reload. You will then be able to stop galaxy using ctrl+c