Keeping Track of Code & Using VS Code¶
A short tooling block on running your QIIME2 work in a way you can actually reproduce six months from now: editing scripts in VS Code with the Remote-SSH connection to Alpine, keeping a running command log, and (optionally) versioning everything with git.
What this lecture covers¶
- Installing VS Code and the Remote - SSH extension
- Connecting to Alpine and editing files on the cluster directly
- Running QIIME2 commands from a
commands.shscript vs typing them ad-hoc - A reproducibility workflow: every command goes in a script, every script goes in a folder you can re-run end-to-end
- Optional: putting that folder under
gitso you can diff your analysis history
Hands-on follow-along¶
For now, the workshop runs commands interactively in the terminal, but make a habit of pasting each command you run into a notes.sh or commands.sh file so you have a re-runnable record.