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Bioconductor / bioc_docker

[DEPRECATED] Docker containers for Bioconductor
https://github.com/bioconductor/bioconductor_docker
Artistic License 2.0
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add cytometry Container #70

Closed mikejiang closed 5 years ago

mikejiang commented 5 years ago

related to #69

lshep commented 5 years ago

It looks like in the config.yml file you updated to include the biocViews: FlowCytometry. Was the intent to make the docker image include all the packages with this biocView term? If so your install script should be updated to something like the src/protmetcore/install.R.in (proteomics and metabolomics install.R.in files also do this) where it uses the biocViews term to filter packages.
Your current install.R.in file would take the base image (which only have BiocManager, Matrix, KernSmooth, mgcv) and then only install the packages you have listed pkgs <- c("biocViews", "CytoML", "roxygen2", "devtools") . This would install the biocViews package not the packages listed under the term specified.

mikejiang commented 5 years ago

I actually do not intend to include all the packages under FlowCytometry term. Instead, we want to narrow down to the core cytometry infrastructure tools maintained by RGLab. CytoML sits at the top of dependency tree thus should cover all the basics users will need.

lshep commented 5 years ago

OK just wanted to double check. I'll continue over merging the pull request and setting up the dockerhub for the new repository - I'll let you know if I run into any issues.

mikejiang commented 5 years ago

Great, thanks a lot!