Hub	Status
Docker
Singularity

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

1. It creates a host directory ~/dockerhome where the home directory of the Docker user will be mounted. Files can be shared between the Docker container and host filesystem here.
2. It results in user-installed packages being added to the host directory ~/.docker-devel-packages or ~/.docker-release-packages.
3. It runs the Docker containers waldronlab/bioconductor_devel and waldronlab/bioconductor_release. The script can, however, easily be changed to use any of the official Bioconductor Docker containers.

The waldronlab/bioconductor_devel and waldronlab/bioconductor_release images are built on top of the bioconductor/devel_base2 and bioconductor/release_base2 images, respectively. They add many system dependencies so that almost every Bioconductor package can be installed using BiocManager::install() with no further troubles. As of the last testing, the release image successfully installed all but 10 of over 1,600 packages (testing done with this gist). For almost everyone, this means no more errors when trying to install a package.

To make a generalization, Docker is more supported by commercial Cloud providers, whereas Singularity is (far) more likely to be supported by university high-performance computing facilities.

If you have singularity installed, pull the singularity images as follows:

singularity pull shub://waldronlab/bioconductor_devel
singularity pull shub://waldronlab/bioconductor_release

So far I have only used singularity for bash and R, with aliases like these (assuming you did the above pull commands from your home directory):

alias singulaR="singularity shell $HOME/waldronlab-bioconductor_devel-master-latest.simg R"
alias singularbash="singularity shell $HOME/waldronlab-bioconductor_devel-master-latest.simg bash"

Note that default behavior in singularity is to mount your home (and several other) directories as the home directory within the container, while maintaining your user permissions. This makes all the docker efforts to mount volumes for your container package and home directories unnecessary. I haven't yet tried running rstudio via singularity, but it shouldn't be too hard?

The following aliases may also be useful in your ~/.bash_profile for command-line R and bash usage with the same containers, package directories, home directory, and rstudio user:

alias releaseshell="docker run -ti -u rstudio -w /home/rstudio -v $HOME/dockerhome:/home/rstudio -v $HOME/.docker-release-packages:/usr/local/lib/R/host-site-library waldronlab/b\
ioconductor_release bash"
alias develshell="docker run -ti -u rstudio -w /home/rstudio -v $HOME/dockerhome:/home/rstudio -v $HOME/.docker-devel-packages:/usr/local/lib/R/host-site-library waldronlab/bioco\
nductor_devel bash"
alias Rrelease="docker run -ti -v $HOME/dockerhome:/home/rstudio -v $HOME/.docker-release-packages:/usr/local/lib/R/host-site-library waldronlab/bioconductor_release R"
alias Rdevel="docker run -ti -v $HOME/dockerhome:/home/rstudio -v $HOME/.docker-devel-packages:/usr/local/lib/R/host-site-library waldronlab/bioconductor_devel R"
#default:                                               
alias R=Rdevel

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. Modify as you see fit, e.g. if you want to mount different directories or in a different place than ~/dockerhome, or change the rstudio password. Make sure the script is executable (e.g. chmod a+x bioconductor).
4. From the command-line, type bioconductor devel or bioconductor release. Later you can use Ctrl-C to stop the container. There are additional usage tips at https://github.com/Bioconductor/bioc_docker, including how to access the image from a command-line.
5. In a browser, open http://localhost:8787. Login with username is "rstudio" and password "rstudiopassword" unless you change the password in the "bioconductor" script of step 3.

That's it! You can stop the instance you're running and switch to release or devel (but you can't currently run both at the same time). There will be separate host package libraries for user-installed packages (in ~/.docker-devel-packages and ~/.docker-release-packages), and a common home directory in ~/dockerhome. docker pull is run each time you invoke the bioconductor script, so you should automatically get the most up-to-date Bioconductor release or devel versions, and will only have to run BiocManager::install() to update user-installed packages.

The bioconductor script is rudimentary and should use docopt, provide start & stop, and have an option for opening a bash shell or R console. It could also provide arguments for the volume location etc.

It at least does error at the docker pull stage if you enter anything other than "release" or "devel" as the argument.