SETUP.md

Setting up the weld

The following are the two setup steps that need to be performed once before starting your first project.

For a general overview of the pipeline welding process, see the repo README.
For the welding process steps to perform with each dataset, see the weld process README.

Setup the computational environment

Setup a new repository

For instructions on how to setup a new repository, see WELD.md

Initialize the computational environment

After setting up a new repository using our template, navigate into the top level directory of the newly cloned repo.

NEW_REPO="INSERT_REPO_NAME_HERE"
cd $NEW_REPO

Install conda.
We use conda as an environment manager.

# Install computational environment
conda env create --force --file environment.yml

# Initialize the environment
conda activate pooled-cell-painting

Fork the Pooled Cell Painting Painting recipe

We first want to fork the official pooled cell profiling recipe located at https://github.com/broadinstitute/pooled-cp-profiling-recipe.

Result:

The fork creates a copy of a recipe repository.

Goals:

1. Remove the connection to the official recipe updates to avoid unintended weld versioning reversal.
2. Enable independent updates to fork code that does not impact official recipe.

Execution:

See forking instructions and the image below.