aquabiota/realm-modelling repository overview

⁠Using the rocker/rstudio container

⁠Quickstart

docker run -d -p 8787:8787 aquabiota/realm-modelling

Visit localhost:8787 in your browser and log in with username:password as rstudio:rstudio.

⁠Notes:

• Based on the rocker/rstudio stack, see: https://github.com/rocker-org/rocker/wiki⁠.

⁠Common configuration options:

Note: all commands documented here work in just the same way with any container derived from aquabiota/realm-rstudio, such as aquabiota/realm-modelling.

⁠Use a custom password by specifying the PASSWORD environmental variable

docker run -d -p 8787:8787 -e PASSWORD=yourpasswordhere aquabiota/realm-modelling

⁠Give the user root permissions (add to sudoers)

docker run -d -p 8787:8787 -e ROOT=TRUE aquabiota/realm-modelling

Link a local volume (in this example, the current working directory, $(pwd)) to the rstudio container:

docker run -d -p 8787:8787 -v $(pwd):/home/rstudio aquabiota/realm-modelling

⁠Add shiny server on start up with e ADD=shiny

docker run -d -p 3838:3838 -p 8787:8787 -e ADD=shiny aquabiota/realm-modelling

shiny server is now running on localhost:3838 and RStudio on localhost:8787.

Note: this triggers shiny install at runtime, which may require a few minutes to execute before services come up. If you are building your own Dockerfiles on top of this stack, you should simply include the RUN command:

RUN export ADD=shiny && bash /etc/cont-init.d/add

Then omit the -e ADD=shiny when running your image and shiny should be installed and waiting on port 3838.

⁠Access a root shell for a running rstudio container instance

First, determine the name or id of your container (unless you provided a --name to docker run) using docker ps. You need just enough of the hash id to be unique, e.g. the first 3 letters/numbers. Then exec into the container for an interactive session:

docker exec -ti <CONTAINER_ID> bash

You can now perform maintenance operations requiring root behavior such as apt-get, adding/removing users, etc.

⁠Additional configuration options

• Custom user name: -e USER=<CUSTOM_NAME>
• Custom user id, group id, UMASK: -e USERID=<UID>, -e GROUPID=<GID>, e UMASK=022

Custom uid/gid etc is usually only needed when sharing a local volume for a user/group whose id does not match the default (1000:1000). Failing to do this could make files change permissions on the linked volume when accessed from RStudio.

Adding additional users: From a root bash shell (see above), the usual debian linux commands can be used to create new users and passwords, e.g.

⁠Developers / Dockerfile authors

The RStudio images use the s6-init system to run multiple/persistant jobs. While init systems like supervisord are better known, s6 is powerful, lightweight, easy to use, and plays nicely with docker (e.g. avoiding the pid 1 / zombie problem). See s6-overlay⁠ for details if you need to add additional services (such as an sshd server) or custom start-up, shut down, or logging scripts.