[Tutorial/Workflow] Using Quarto Notebooks with VSCode & Python

[TinasheMTapera]

Issue: I needed to install Quarto on the cluster to use with VS Code and Python.

Note: If you want to use Quarto in RStudio Server, it is already installed, and no additional action should be required.

Solution and context provided by FASRC:
FASRC is no longer installing software globally as modules because that practice became unsustainable -- we were managing over 6000 modules. We offer modules for proprietary software that require licensing, as well as major compilers and programming languages. For all other software, we are empowering users to build their own software. I was able to install Quarto by modifying their Linux install instructions. These were the steps on the cluster:

1. Go to a directory where you would like to install your software (e.g. ~/software or /n/holylabs/cgolden_lab/Lab/software -- note that "software" folder needs to be created).
2. wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.7.32/quarto-1.7.32-linux-amd64.tar.gz
3. tar -xvzf quarto-1.7.32-linux-amd64.tar.gz
4. cd quarto-1.7.32/bin
5. pwd
6. copy the output of pwd
7. export PATH=$PATH:

Example for steps 4-7:
[paulasan@holylogin06 software]$ cd quarto-1.7.32/bin/
[paulasan@holylogin06 bin]$ pwd
/n/home_rc/paulasan/software/quarto-1.7.32/bin
[paulasan@holylogin06 bin]$ export PATH=$PATH:/n/home_rc/paulasan/software/quarto-1.7.32/bin

I recommend that you add the export command (export PATH=$PATH:) in your ~/.bashrc file so that Quarto is always included in your PATH. Otherwise, you will have to execute the export command every time you login to the cluster or submit a job.

Finally, you can then test if Quarto works with:
[paulasan@holylogin06 bin]$ quarto check

[TinasheMTapera]

Fairly straightforward, can go into a general "installing software" section where we mention that FASRC only moderates licensed software; all else is free for all so long as it doesn't require root