Image-based Profiling Template

This repository was derived from a template repository located at https://github.com/cytomining/profiling-template. The purpose of the repository is to weld together a versioned data processing pipeline with versioned processed output data for a single image-based profiling experiment.

(Derived from this template)

AFTER GENERATING A NEW REPO, CHANGE OR DELETE ALL NONSPECIFIC DETAILS

Setup

To correctly initialize the repository, we need to perform several manual steps.

Step 0: Create a new repository using this repository as a template

By spinning up a new repo using this repo as a template, you will retain all code, configuration files, computational environments, and directory structure that a standard image-based profiling workflow expects and produces.

Step 1: Fork the profiling-recipe repo

We first want to fork the official profiling recipe located at https://github.com/cytomining/profiling-recipe.

• Result: The fork creates a copy of a recipe repository.
• Goals: 1) Remove the connection to 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.

Step 2: Create a submodule inside this repository of the forked recipe

Next, we will create a submodule in this repo.

• Result: Adding a submodule initiates the weld.
• Goals: 1) Link the processing code (recipe) with the data (current repo); 2) Require a manual step to update the recipe to enable asynchronous development.
• Execution: See below

# In your terminal, clone the repository you just created (THIS REPO)
USER="INSERT-USERNAME-HERE"
REPO="INSERT-NAME-HERE"
git clone [email protected]:$USER/$REPO.git

# Navigate to this directory
cd $REPO

# Add the recipe submodule
git submodule add https://github.com/$USER/profiling-recipe.git profiling-recipe

Refer to "Adding a submodule" for more details.

Step 3: Commit the submodule

Lastly, we will commit the submodule to github.

• Result: Committing this change finalizes the weld.
• Goals: 1) Track the submodule (recipe) version with the current repository.
• Execution: See below

# Add, commit, and push the submodule contents
git add profiling-recipe
git add .gitmodules
git commit -m 'finalizing the recipe weld'
git push