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A Django web app over an RDF phylogeny database supporting tree annotation and querying.
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apache
phylocommons
tools
treequery
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LICENSE
Makefile
README.md
create_profiles.py
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manage.py

README.md

PhyloCommons

PhyloCommons is a Django web application frontend to the RDF treestore, which stores phylogenetic trees in a triple store for easy reuse.

Installing your own instance of PhyloCommons

Django

You'll need Django version 1.4 installed. PhyloCommons uses the django-registration plugin which is not currently compatible with Django 1.5.

Virtuoso

You'll also need OpenLink Virtuoso installed, which is used to store the trees.

Virtuoso needs to be configured to be able to load trees from a directory called "treestore" inside your temporary file directory - on Unix systems, this will be /tmp/treestore. Add this directory to the DirsAllowed parameter in Virtuoso's virtuoso.ini configuration file. It should look something like this:

DirsAllowed                     = ., /usr/share/virtuoso/vad, /tmp/treestore

Installation

Clone the repository and initialize the submodules:

git clone https://github.com/bendmorris/phylocommons
cd phylocommons
git submodule init
git submodule update

To install PhyloCommons, run make from the root directory. This will install the prerequisites (rdf-treestore and biopython) if they aren't already present, create the SQLite database, and set up the settings/secret key files.

To create a superuser account and configure the installation, pass variables to make:

make username='bendmorris' email='ben@bendmorris.com'`

Variables that can be specified include:

  • username: the username of the superuser (will be created without a password)
  • email: the email address of the superuser
  • domain: the domain the site will run from (e.g. http://www.phylocommons.org/)
  • treestore_kwargs: a python dictionary of keyword arguments to be passed to the RDF treestore; common options are 'dsn', 'user', and 'password'

Testing

To test PhyloCommons:

  • start Virtuoso
  • run python manage.py runserver
  • navigate to localhost:8000 in your web browser
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