Hello,
I would like to try an experiment where I use the CLI in Galaxy via Interactive JupyterLab Notebook to do an RNA-seq alignment using histat2 or STAR. However, whenever I use either these in the terminal I get “command not found”. I have not be able to find a clear answer online as to why these are automatically available on the command line in this instance.
Can someone please advise me as to what to do next? Thanks.