These Docker images are built on the corresponding devel or RELEASE_X_Y branches of Bioconductor's base Docker image with the the following additional packages installed (along with their dependencies).
- RProtoBufLib: GitHub, Bioconductor
- cytolib: GitHub, Bioconductor
- flowCore: GitHub, Bioconductor
- flowViz: GitHub, Bioconductor
- ncdfFlow: GitHub, Bioconductor
- flowWorkspace: GitHub, Bioconductor
- flowWorkspaceData: GitHub, Bioconductor
- flowClust: GitHub, Bioconductor
- flowStats: GitHub, Bioconductor
- ggcyto: GitHub, Bioconductor
- openCyto: GitHub, Bioconductor
- CytoML: GitHub, Bioconductor
This is provided as an option to make it easier for users of all platforms to use the packages for analysis of cytometry data without needing to worry about dependencies or platform-dependent aspects of installation. It will also be continuously updated to the newest versions of the packages, allowing users to stay up to date with a single docker pull command.
rglab/cytoverse:devel will be automatically built off of biconductor/bioconductor_docker:devel, using the most up-to-date development branches of the Cytoverse packages.
rglab/cytoverse:RELEASE_X_Y (where X and Y are major and minor Bioconductor release version numbers) are built on the corresponding bioconductor/bioconductor_docker:RELEASE_X_Y using the corresponding release branches of the Cytoverse packages.
Please see Docker's documentation for general notes on using containers and getting started with installation on your system
As these Docker images are built directly on the Bioconductor docker image, they can be used in the same way, with the only difference being that
you will already have access to the additional packages listed above. Please see see the documentation on Bioconductor Docker regarding usage. To obtain the Cytoverse docker images to run in a container locally, simply execute the following command (in this case using the devel branch as an example):
docker pull rglab/cytoverse:devel
You can then run the container and make an RStudio session available in the same way as for the base Bioconductor image:
docker run \
-e PASSWORD=bioc \
-p 8787:8787 \
rglab/cytoverse:devel
This will make an RStudio session available using a web browser at https://localhost:8787. The user will be rstudio and the password will be bioc.
For further information on additional topics including mounting storage volumes or modifying the images (for example adding in more packages), please consult the Bioconductor Docker documentation.