Project Setup
Owner: Gaby
Standard setup for a new dry-lab project, start to finish.
1. Assign a Project ID
When initiating a new analysis project (ex. single-cell, spatial, etc.,), refer to the Project Management Sheet on box. Follow the instructions below for adding a new project ID to the management sheet.
Format: prj#### — first 2 digits = last 2 digits of year; last 2 digits = next sequential number. Example: if last ID is prj2604, next is prj2605.
2. Acquire the Metadata Sheet
For tracking sample metadata, use the Cheng Lab sample metadata template, which can be found on Box.
3. Create the Project Folder
On the PMACS server, create a folder named for the project ID under the appropriate lab project space (all analyses containing patient data should be performed in the hipaa_ycheng11lab directory): /project/ycheng11lab/
4. Create Your Own Subfolder
Inside the project folder, create a subfolder under your PennKey/username: /project/ycheng11lab/
Do your compute here — keep intermediate/working files scoped to your own subfolder so the shared project folder stays organized (see Lab Duties — Jeff’s server-cleanup responsibilities depend on this).
5. Push Scripts to the Lab GitHub
Code/scripts (not data) go to the lab-manual org’s project repos, not the server. See Lab Tutorials → GitHub Usage for the actual git workflow.
Keep large or sensitive data out of git — see the .gitignore conventions in GitHub Usage.
6. Using a Coding Agent
If you’re using a coding agent (Claude Code, Codex, etc.) to help with the project, see: