About the "bioconductor" script

This script makes it more convenient to run the Bioconductor docker images locally for routine daily usage:

% ./bioconductor -h
Usage: bioconductor.sh [-v version] [-e envtype] [-p port] [-w password] [-d dockerhome] [-l] [-h]
  -v version    Specify the Bioconductor version (e.g., 'devel', 'RELEASE_X_Y', 'X.Y').
  -e envtype    Specify the environment type ('rstudio', 'bash', or 'R'). Default is 'rstudio'.
  -p port       Specify the port number. Default is 8787.
  -w password   Specify the RStudio password. Default is 'bioc'.
  -d dockerhome Specify the Docker home directory. Default is '"$HOME"/dockerhome'.
  -l            List all available Bioconductor Docker versions.
  -h            Show this help message.

The $DOCKER_RPKGS environment variable is optional and used to specify the R packages directory on the host machine.
If not set, the default is '$HOME/.docker-$version-packages'.
This directory is mounted into the Docker container at /usr/local/lib/R/host-site-library.
This allows R packages installed in the container to be persisted on the host machine and shared across multiple containers or sessions.

This script makes it easy to:

1. Run any version of Bioconductor represented by a tag at https://hub.docker.com/r/bioconductor/bioconductor_docker/tags
2. Run command-line R, bash, or RStudio
3. Have a persistent local packages directory for every version of Bioconductor, and map the container home directory to a specified local directory.
4. Specify the port and password for RStudio
5. List all available Bioconductor versions

About the bioconductor_docker docker image

The bioconductor/bioconductor_docker image is built for both release and devel versions of Bioconductor. It includes system dependencies so that almost every Bioconductor package can be installed using BiocManager::install() with no further troubles. For almost everyone, this means no more errors when trying to install a package.

Using the bioconductor script and docker container

1. Install a docker client for your operating system.
2. Make sure home directories are being shared (Whale icon -> Preferences -> File Sharing). Last I checked, this was already the case by default. You can also change the allotted system resources if you want.
3. Copy the bioconductor script from this repo to somewhere in your $PATH. Make sure the script is executable (e.g. chmod a+x bioconductor).
4. From the command-line, type bioconductor -h to make sure it's working, then get started. There are additional usage tips at https://github.com/Bioconductor/bioc_docker.

That's it! You can use Ctrl-C (Cmd-C on OSX) to stop the RStudio server.