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 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
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.
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.
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)
- clone or downlad and extract this repository
- cd ReproPhyloGalaxy
You will be asked for sudo password
Note: After the installation is done the repository directory can be removed
- cd ~/galaxy-dist
- sudo sh run.sh
- 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