Shiny App from the hackathon of reelGene scores and other data
ReelGene is currently running on the "BucklerHub" JupyterHub server hosted on a VM in CBSU/BioHPC. To make use of the resources we already have, during hackathon this server was used to also host reelGene.
The BucklerHub runs The Littlest JupyterHub, which uses Traefik as a reverse proxy to direct users to their own Jupyter servers that are spun up.
TLJH allows you to add additional routes to Traefik by adding a .toml file in /opt/tljh/state/rules (docs here). We utilize this feature to direct requests for https://reelgene.maizegenetics.net to the Shiny Docker containers. The specific config file we are using is reelgene.toml in this repository (less the hashed password).
In order to keep reelGene private before publication, we are using HTTP "Basic" Authentication to provide a rudimentary login window before displaying the application. For example, if we wanted to login with username spaghetti and password tasty, we use htpasswd to generate a hash to enter into our config:
$ htpasswd -nbB spaghetti "tasty"
spaghetti:$2y$05$bajwHRzDUuGQWSkFayXZruhrGCYRvSdC7zfnl2vRlwohy5gRyhsCK
Copy the output and modify the file like so:
[frontends.reelgene.auth.basic]
users = [
"spaghetti:$2y$05$bajwHRzDUuGQWSkFayXZruhrGCYRvSdC7zfnl2vRlwohy5gRyhsCK"
]The configuration makes Traefik aware of four "servers" at ports 8001 - 8004 to which it distributes traffic in a round-robin fashion. htpasswd uses bcrypt to hash passwords by default. It includes salt, such that generating a hash for the same combination results in unique hashes each time. In theory, it should be safe to commit this hashed password (but let's not do that).
The four servers that load is distributed to correspond to four identical containers on the machine. These containers are managed through a simple Docker Compose file, docker-compose.yml. To bring up the four containers just do:
docker compose up -d
The -d flag is to detach the containers from our current shell, so they run "in the background."
The containers themselves are built from this repo's Dockerfile which is based upon rocker/shiny-verse with the additional required packages from CRAN and Bioconductor installed.