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RStudio Password

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2 comments

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    Jason Cerrato

    Hi Nicholas,

    Thank you for your question. Let me check in with the notebooks team on this and get back to you!

    Kind regards,

    Jason

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    Jason Cerrato

    Hi Nicholas,

    To install packages, you will need to set up a docker image that pre-installs them, or provide a startup script to the runtime. A startup script is the easiest way to add package.

    Here is an example of what the contents of a startup script could look like:

    #!/usr/bin/env bash

    pip install nbconvert
    apt-get update
    apt-get install -yq pandoc texlive-xetex
    R -e "install.packages('devtools')"
    pip install scanpy[louvain]==1.4.4.post1 anndata==0.6.22rc1 h5py==2.9.0
    R -e "BiocManager::install('multtest')"

    For any R packages of interest you will want to use the R -e notation. Once you have the script loaded into a Google bucket (like the workspace bucket) you simply provide the gs:// path to the Startup script box.

     

     

    Once you create the runtime with the script, both R and RStudio will have access to the installed packages.

    You may also be interested in reading more about the RStudio image we use. You can find that information here: https://github.com/anvilproject/anvil-docker/tree/master/anvil-rstudio-bioconductor

    Kind regards,

    Jason

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