waldronlab/bioconductor_devel repository overview

Hub	Version	Status
Docker
Docker
Docker

⁠About the "bioconductor" script

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 container bioconductor/bioconductor_docker⁠

⁠Inputs to the 'biconductor' script

The user must specify the version of Bioconductor to spin up as a Docker image. The available inputs for the first argument are:

1. release
2. devel

The second argument for the 'bioconductor' script denotes the environment type to run when executing the script this will either put the user in one of two supported environements:

1. rstudio - allows the user to open up an rstudio session in the browser
2. shell - put the user in the command line within the container

Note. The default user environment is the rstudio session

⁠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.

⁠For singularity users

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 and the singularity images as follows (or substitute "devel" with "release" for the release version):

singularity build $HOME/bioconductor-devel.img docker://waldronlab/bioconductor:devel

So far I have only used singularity for bash and R, with aliases like these:

alias singulaR="singularity shell $HOME/bioconductor-devel.simg R"
alias singularbash="singularity shell $HOME/bioconductor-devel.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 should be possible?

⁠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. 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.
5. If using the 'rstudio' argument (default) --- In a browser, open http://localhost:8787⁠. Login with username is "rstudio" and password "rstudiopassword" unless you change the password within the "bioconductor" script in 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.

Note: Checking mechanisms have been implemented for the script to error if anything other than "release" or "devel" is entered in the first argument.

⁠Example command line execution

The following commands may 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="bioconductor release shell"
alias develshell="bioconductor devel shell"

# coming soon #
alias Rrelease="bioconductor release R"
alias Rdevel="bioconductor devel R"

⁠TODO

The bioconductor script is rudimentary and should use docopt, and provide start & stop. It could also provide arguments for the volume location etc.