Add reverse proxy for bioconductor (R)

[AaronJackson]

No description provided.

[AaronJackson]

I had been working on a test

  - name: bioconductor package installation
    shell:
      cmd: |
        #rm -rf /usr/local/lib/R/site-library/dplyr # remove if installed
        /usr/bin/R --no-save <<RPROG
        install.packages("BiocManager")
        options(BIOCONDUCTOR_CONFIG_FILE="file:///root/config.yaml")
        options(BioC_mirror="http://bioconductor.localhost")
        options(BIOCMANAGER_SITE_REPOSITORY="http://bioconductor.localhost")
        library(BiocManager)
        BiocManager::install("BiocVersion")
        q()
        RPROG
        #ls /usr/local/lib/R/site-library/dplyr
    failed_when: false
    changed_when: false
    register: bioc_install

but it doesn't work in this version of ubuntu (like the other R CRAN test). R is too old. I might look at changing ubuntu version next week.

I also need to figure out what to do about config.yaml. It would be nice if we could proxy that too. It comes from bioconductor.org/config.yaml regardless of the mirror, but can be overridden. I couldn't reverse proxy bioconductor.org directly

[AaronJackson]

No idea if this will actually work from TRE workspaces, very confidence inspiring

[manics]

Seems fine to me!