RMDB RNA Mapping DataBase

This is the Source Code repository for RMDB RNA Mapping DataBase Server. The production server is freely accessible at https://rmdb.stanford.edu/.

Installation

RMDB Server requires the following Python packages as dependencies, most of which can be installed through pip.

boto >= 2.38.0
Django >= 1.9.1
django-adminplus >= 0.5
django-crontab >= 0.7.0
django-environ >= 0.4.0
django-filemanager == 0.0.2
django-suit >= 0.2.15
django-widget-tweaks >= 1.4.1
gviz-api.py == 1.8.2
MySQL-python >= 1.2.5
PyGithub >= 1.26.0
pytz >= 2015.7
requests >= 2.9.1
simplejson >= 3.8.1

rdatkit >= 1.0.2

The rdatkit package is available internally at https://github.com/ribokit/rdatkit/.

The gviz-api.py is available at https://github.com/google/google-visualization-python/.

The django-filemanager is a modified version of https://github.com/IMGIITRoorkee/django-filemanager/. The source code is available internally. Install with sudo python setup.py install.

RMDB Server also requires proper setup of imagemagick, optipng, VARNA.jar, mysql.server, apache2, mod_wsgi, openssl, gdrive, awscli, and cron jobs.

Lastly, assets preparation is required for the 1st time through running sudo python manage.py versions, sudo python manage.py dist, util_prep_dir.sh, util_src_dist.sh, util_minify.sh, util_chmod.sh and manually replacing config/*.conf. For full configuration, please refer to Documentation.

Usage

To run the test/dev server, use:

cd path/to/server_RMDB/repo
python manage.py runserver

Documentation

Documentation is available at admin manual and reference.
Alternatively, read the repository Wiki.

License

RMDB Server Source Code is proprietary and confidential. Unauthorized copying of this repository, via any medium, is strictly prohibited.

Reference

Cordero, P., et al. (2012)
An RNA Mapping DataBase for Curating RNA Structure Mapping Experiments.
Bioinformatics 28 (22): 3006-3008.