vgbrowser

Browser for Graph Genomes built with VG. Provides visualization for variation within a species of plant or animal. Designed to scale up to thousands of specimens and provide useful visualizations.

Backend: Toshiyuki Yokoyama \ Client-Server-Communication and Drawing: Simon Heumos \ Algorithms and Design: Josiah Seaman

Developer Instructions

Environment: Anaconda 3.7
Ggfapy etc. does not have an anaconda package, so it's necessary to use pip:
pip install -r requirements_dev.txt

IDE: Pycharm Professional 2019.1 available for free for academics.

• Travis CI - automatically runs tests on master and development branches
• Jupyter Notebook - run from the same Anaconda environment. Notebooks are useful for prototyping, mature code gets moved to .py files for reuse. They can be matured into a user manual.

Django: This project uses django for its relational database. db.sqlite3 is not included in the repo. You will need a super user to be able to browse the database in the administrator backend. To setup Django database file run

python manage.py migrate
python manage.py createsuperuser

In development, changes to the models.py need a new migration created using
python manage.py makemigrations

Branches

master - should always run tests without errors. This is currently our development branch until our first release. Only use Pull Requests to update master. We will do code review on master.
development - Future branch once we have our first release point. Staging for master, stable. Travis tests should pass, if they don't work to fix this first. Only use Pull Requests to update development branch.
other branches - create your own for developing on a specific issue. For Issue #3 i3_graph_summarization. You can merge these manually.