AraGeno

AraGeno is a django web-application for allowing researchers to easily run SNPmatch using the web-browser. The user only needs to upload a VCF or BED file. The analysis will be run on a HPC that needs to be configured seperately.

Installation & Usage

The below steps only deal with the web-application part. In order to run AraGeno, also SNPmatch must be installed on a HPC and configured properly

Using pip:

git clone git@github.com:Gregor-Mendel-Institute/AraGeno.git 
cd AraGeno
pip install -r requirements.txt

Run the django web-app:

./manage runserver

Run the listener for the HPC jobs:

./manage.py listen_job_queue 'amqp://AMQP_BROKER'

Using docker/docker-compose:

Create .env file for environment variables:

EMAIL_HOST=[EMAIL_HOST]
EMAIL_USER=[EMAIL_USER]
BROKER=[AMQP BROKER FOR JOB INFOS]
HPC_USER=[HPC_USER]
ALLOWED_HOSTS=[ALLOWED_HOSTS]
SECRET_KEY=[SECRET]

Checkout code and ruin docker-compose:

git clone git@github.com:Gregor-Mendel-Institute/AraGeno.git 
cd AraGeno
docker-compose up -d 

Contributing

1. Fork it!
2. Create your feature branch: git checkout -b my-new-feature
3. Commit your changes: git commit -am 'Add some feature'
4. Push to the branch: git push origin my-new-feature
5. Submit a pull request :D

History

• 0.0.1: Initial implementation

Credits

• Ümit Seren (uemit.seren[at]gmi.oeaw.ac.at)
• Rahul Pisupati (rahul.pisupati[at]gmi.oeaw.ac.at)
• Ilka Reichardt-Gomez (ilka.reichardt[at]gmi.oeaw.ac.at)
• Envel Kerdaffrec (envel.kerdaffrec[at]gmi.oeaw.ac.at)

License

MIT license