Primerize PCR Assembly Design Server

This is the Source Code repository for Primerize PCR Primer Assembly Design Server. The production server is freely accessible at https://primerize.stanford.edu/.

Installation

Primerize 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

primerize >= 1.1.0

The primerize package is available internally at Primerize.

The gviz-api.py is available at google-visualization-python.

The django-filemanager is a modified version of django-filemanager. The source code is available internally at this fork.

Install with:

cd ~
git clone https://github.com/ribokit/Primerize.git
cd Primerize
sudo python setup.py install

cd ..
git clone https://github.com/google/google-visualization-python.git
cd google-visualization-python
sudo python setup.py install

cd ..
git clone https://github.com/t47io/django-filemanager.git
cd django-filemanager
sudo python setup.py install

Primerize Server also requires proper setup of llvm, 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_primerize/repo
python manage.py runserver

The server should be running at localhost:8000 with a python session interactive in terminal.

Documentation

• Documentation is available at admin manual and reference.

• Alternatively, read the repository Wiki.

License

Copyright © 2014-2017: Siqi Tian [t47], Das Lab, Stanford University. All Rights Reserved.

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

Copyright © of Primerize Source Code is described in LICENSE.md.

Reference

Tian, S., et al. (2015)
Primerize: Automated Primer Assembly for Transcribing Interesting RNAs.
Nucleic Acid Research 43 (W1): W522-W526.

Tian, S., and Das, R. (2017)
Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
Bioinformatics 33 (9): 1405-1406.

by t47, August 2016.