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@@ -149,3 +149,50 @@ Here we convert such a pipeline into the Common Workflow Language (CWL) and sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate). For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). + +# Web Interface + +This project comes with a simple web server that lets you use the sequence uploader from a browser. It will work as long as you install the packager with the `web` extra. + +To run it locally: + +``` +virtualenv --python python3 venv +. venv/bin/activate +pip install -e .[web] +env FLASK_APP=bh20simplewebuploader/main.py flask run +``` + +Then visit [http://127.0.0.1:5000/](http://127.0.0.1:5000/). + +## Production + +For production deployment, you can use [gunicorn](https://flask.palletsprojects.com/en/1.1.x/deploying/wsgi-standalone/#gunicorn): + +``` +pip3 install gunicorn +gunicorn bh20simplewebuploader.main:app +``` + +This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments) + +## GNU Guix + +To run the web uploader in a GNU Guix environment + +``` +guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run +``` + +The containerized version looks like + +``` +guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl +``` + +and + +``` +env FLASK_APP=bh20simplewebuploader/main.py flask run +``` + |