The Wizard

cis-gs wizard

Launches an interactive walkthrough of the entire 7-step pipeline. The wizard:

  • Auto-detects what you’ve already produced in ~/CisGS-Workspace/.

  • Offers the next sensible step (e.g. “You already ran Step 2; want to run Step 3 logos now?”).

  • Uses arrow keys + Enter for every choice — no flag memorisation.

  • Falls back to text input where free-form values are required.

  • Saves your last answers to ~/CisGS-Workspace/.wizard_state so a re-run resumes where you left off.

Sample session

$ cis-gs wizard

Welcome to Cis-GS v1.1.0
--------------------------
Which step would you like to run?

  > 1. Promoter extraction
    2. Motif search
    3. Motif logos
    4. Expression feeding
    5. Co-expression network
    6. K-means clustering
    7. KEGG enrichment

[Enter] continue   [q] quit