Episb hub

User documentation can be found at http://code.databio.org/episb

Running the app for development

FLASK_APP="main.py" flask run

Point browser to http://localhost:8888/

Running the app in a container

To build the episb-hub container locally and test, follow these steps:

1. In the same directory as the Dockerfile:

$ docker build -t <docker image>:<tag optional> .

2. Run the container from the image you just built:

$ docker run -d -p 80:80 --rm --name episb-hub <docker image>:<tag>

3. Interact with and preview the site: http://localhost/

4. When done, stop the container:

$ docker stop episb-hub

Running the app in a container with development mode

To run the container and have it reflect the changes, use the Dockerfile_dev to build the image:

$ docker build -f Dockerfile_dev -t episb .

To run the container:

$ docker run -v /path/to/host/episb-hub:/app -p 80:80 --rm --name episb-hub -e FLASK_APP=main.py -e FLASK_DEBUG=1 episb flask run --host=0.0.0.0 --port=80

Now the development container will be viewable on your localhost and update with any changes you make.

ElasticSearch

Note that this site requires ElasticSearch indices as a data provider for regions, experiments, segmentations, etc. Flask looks for ES indices at port 8080 of the localhost.

Docs:

These docs can be rendered locally for development with:

mkdocs serve -f mkdocs.yml

And can be built for deploy with:

RENDERED_DIR="$CODEBASE/code.databio.org/episb"
mkdocs build -f episb-docs/mkdocs.yml -d "$RENDERED_DIR"

Or by running update_docs.sh.