dtenenba/cytoscape repository overview

⁠Exploratory Docker containers related to the Bioconductor project

NOTE: Containers which will be officially suported can be found at https://github.com/Bioconductor/bioc_docker⁠; containers in this repository are not of general interest as they are for internal Bioconductor projects.

See the README.md file in each directory for more detailed information.

Several of these containers are hosted on Docker Hub (as automated builds) and can be downloaded with docker pull.

⁠rserve_client_devel and rserve_server_devel

Simple proofs-of-concept for the idea of using an Rserve instance do do some work using functions of a package that can take a long time to load. If the instance of Rserve is already running with the package loaded, then the client can send expressions to the server with a very quick response. We use this scenario in our Galaxy tools when we want them to run a fast calculation, where the calculation runs much faster than the time it takes to load the packages necessary to run the calculation. Now that Galaxy supports running tools inside Docker, this same scenario can still be realized by having the rserve_server_devel container running with the name server, then running the galaxy tool with the added job.conf parameter --link server:server (supported in this changeset⁠).

TODO: Add a fig.yml to illustrate use of these containers (not necessarily in a a Galaxy context).

⁠Utilities

⁠./get_url.sh

When you run a container that exposes a web server, this script will give you the URL to the server, with the appropriate host and port.

⁠b2on and b2off

For Mac users of boot2docker.

b2on starts the boot2docker vm (if it's not already on) and sets some environment variables that are required in any shell where you will be working with Docker. It also adds [dk] to the beginning of your shell prompt to indicate that this has been done.

b2off turns off the boot2docker vm, unsets the environment variables, and returns your shell prompt to normal.

IMPORTANT: These scripts need to be run by sourcing them with the . command, for example:

. b2on
. b2off

If you like, you can add aliases that do this to your ~/.bash_profile.

⁠Containers for Internal Use

NOTE: The following containers are for internal Bioconductor core team projects only and would probably not be of interest to the wider Bioconductor community.

⁠support.bioconductor.org

A development environment for the Bioconductor support site.

⁠bioconductor.org

A development environment for the Bioconductor website.

⁠tracker.bioconductor.org -

A development environment for the bioconductor issue tracker. This is in its infancy and issues may arise.