This is the Source Code repository for RMDB RNA Mapping DataBase Server. The production server is freely accessible at https://rmdb.stanford.edu/.
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.
To run the test/dev server, use:
cd path/to/server_RMDB/repo
python manage.py runserver
Copyright © 2014-2016: Siqi Tian [t47], Das Lab, Stanford University. All Rights Reserved.
RMDB Server Source Code is proprietary and confidential. Unauthorized copying of this repository, via any medium, is strictly prohibited.
Cordero, P., et al. (2012)
An RNA Mapping DataBase for Curating RNA Structure Mapping Experiments.
Bioinformatics 28 (22): 3006-3008.
by t47, March 2016.