Xing-lab imaging analysis pipeline

How to use this repository

To clone this repository on cluster and setup your github account on CSB cluster, please follow the instructions here: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent

Please follow the instructions in guide.md

Slurm Script Conventions and Tricks

• Assume script paths relative to this repository root
  • submit sample slurm jobs at root directory of this repository
• hacky tricks on PITT CSB cluster
  • please submit in conda base environment or without conda env activated, or the job conda env will not be activated environment correctly and your job is probably going to fail.
  • in slurm scripts, use source instead of conda cmd to activate environments. source activation method should have been deprecated and conda is preferred according to the conda official website. However... Anyway this is our current cluster status.

Install Precommit Hook (For developers/contributors only)

You would like to ensure that the code you push has good code style
This step enables pre-commit to check and auto-format your style before every git commit.

Install (once)

pip install pre-commit
pre-commit install

format all code (rare usage)

pre-commit run --all

Development guide

Avoid copying code files and push identical code

Avoid copying other package's python code directly