RStudio Password
Hi all! I was trying to install boost libraries while running RStudio on Terra, however it requires a password for me to gain root access. Is there a way to access the password?
Hi all! I was trying to install boost libraries while running RStudio on Terra, however it requires a password for me to gain root access. Is there a way to access the password?
Comments
2 comments
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
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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