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.
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
git clone [email protected]:Gregor-Mendel-Institute/AraGeno.git
cd AraGeno
pip install -r requirements.txtRun the django web-app:
./manage runserverRun the listener for the HPC jobs:
./manage.py listen_job_queue 'amqp://AMQP_BROKER'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 [email protected]:Gregor-Mendel-Institute/AraGeno.git
cd AraGeno
docker-compose up -d - Fork it!
- Create your feature branch:
git checkout -b my-new-feature - Commit your changes:
git commit -am 'Add some feature' - Push to the branch:
git push origin my-new-feature - Submit a pull request :D
- 0.0.1: Initial implementation
- 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)
MIT license