04 - MitoPilot installation

First-time installation

To install MitoPilot, run the following commands within RStudio (in the R console, not the terminal). First time installation will take a while.

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("Smithsonian/MitoPilot", ask = FALSE) # "ask = FALSE" to automatically install dependencies

You may see a warning like this:

Installation paths not writeable, unable to update packages
  path: /share/apps/bioinformatics/R/4.4.1/lib64/R/library

This is not a problem. Some R packages are installed at the Hydra system level and cannot be updated by the user.

If there were no other error messages, you’re ready to start using MitoPilot!

Updating MitoPilot

If you need to update MitoPilot, run the following commands in RStudio server.

remove.packages("MitoPilot")
BiocManager::install("Smithsonian/MitoPilot")
.rs.restartR()

This will remove the old MitoPilot package, install the most recent version, and restart your R session. After updating, you will need to reload the package with library(MitoPilot).

We also recommend clearing your Singularity cache with singularity cache clean whenever you update MitoPilot. This will ensure you are using the latest MitoPilot Singularity image.