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

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

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.