Revert "update README for #10"

This reverts commit 1ee5431.

README.md

@@ -1,3 +1,112 @@
-## 2024 June: Childhood Cancer Data Lab "Introduction to Single-Cell RNA-seq" Workshop
+# training-specific-template
+
+This repository is intended to serve as a template for creating a repository for an individual Data Lab workshop.
+The repository structure and use of GitHub Pages is intended to gather all material required to administer a workshop in one user-friendly place.
+We use a template repository approach for maintainability.
+
+Please refer to [`CONTENTS.md`](./CONTENTS.md) for a brief overview of this repository's contents.
+
+## Creating a repository for an individual training workshop
+
+First, you will need to create a new repository using the [`Use the template` button](https://help.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-from-a-template).
+This will create a new repository with the same layout as this template repository under the user or organization you choose as the owner of the repository; if you are a Data Lab member running an internal training workshop, the `AlexsLemonade` organization should be the owner.
+
+### Turning on required settings
+
+
+1. Ensure you have the correct [visibility setting](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/managing-repository-settings/setting-repository-visibility) for your GitHub account tier.
+    * If you are using GitHub from a **paid account tier** (e.g., GitHub Pro, GitHub Team, or GitHub Enterprise), you can set the visibility of this repository as either public or private; the associated GitHub Pages website will still be public.
+    * If you are using GitHub from a **free account tier** (e.g., GitHub Free for individuals or organizations), you must set the visibility of this repository as **public** for [GitHub Pages to be active](https://docs.github.com/en/pages/getting-started-with-github-pages/about-github-pages).
+
+2. Turn on workflow permissions for GitHub Actions.
+    * There are several [manually-triggered GitHub Actions](https://docs.github.com/en/actions/using-workflows/manually-running-a-workflow) provided to facilitate setting up this new repository.
+    * You must turn on "Read and Write" permissions for GitHub Actions to use them:
+      * Navigate to the repository's "Settings" tab at the top of the page.
+      <br><img src="./images/github_bar_settings.png" alt="Actions tab" width="600"/><br>
+
+      * Navigate to the `Actions` -> `General` page from the sidebar
+      <br><img src="./images/actions_general.png" alt="General actions settings" width="200"/><br>
+
+      * Ensure [the following settings](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/enabling-features-for-your-repository/managing-github-actions-settings-for-a-repository#configuring-the-default-github_token-permissions) are turned on:
+        <br>
+        <img src="./images/workflow-permissions.png" alt="Workflow permissions settings to turn on" width="600"/>
+
+
+
+## Customizing the new repository for an individual training workshop
+
+The first step of setting up up this repository is to run the [manually-triggered GitHub Action](https://docs.github.com/en/actions/using-workflows/manually-running-a-workflow) "Manually trigger issue creation for standard set up" GitHub action.
+When triggered, this action will file a series of issues comprising tasks that should be completed before the start of a workshop.
+
+Run this action as follows:
+
+* Navigate to the repository's "Actions" tab at the top of the page.
+<br><img src="./images/github_bar_actions.png" alt="Actions tab" width="600"/><br>
+
+* On the upper left-hand side, you will see all available workflows.
+* Click the workflow named `Manually trigger issue creation for standard set up`, and then click the "Run workflow" dropdown button.
+  * You will see a dropdown button "Use workflow from"; ensure this says the default branch `main`: <img src="./images/run-workflow-from-main.png" alt="Run workflow from main branch" width="300"/>
+
+To complete repository setup, address all issues filed by this workflow.
+
+## Local development
+
+It can be helpful to build the GitHub Pages site locally to check that passing parameter values is working as expected.
+
+### Installing GitHub Pages dependencies locally
+
+Installing the dependencies for GitHub Pages is best done in a separate ruby environment, managed by [`rbenv`](https://github.com/rbenv/) and [Bundler](https://bundler.io)
+
+The following instructions were tested for installation on macOS, but installation on other systems should be similar.
+
+1. [Install `rbenv`](https://github.com/rbenv/rbenv#installation).
+The easiest, and recommended, installation is through [Homebrew](https://brew.sh/):
+```
+# install rbenv
+brew update
+brew install rbenv ruby-build
+```
+Alternatively, you can install with [`rbenv-installer`](https://github.com/rbenv/rbenv-installer#rbenv-installer) which will work even without Homebrew (though it uses Homebrew if you have it).
+
+2. Install `rbenv` for your shell.
+Since this will depend on which shell you are using, you will want to run `rbenv init` to find the correct command to add you your shell configuration file.
+Note that this command does _not_ actually perform the initialization: it only prints instructions for what line to add to which file!
+Be sure to add that line to the _end_ of the configuration file indicated.
+
+4. Once you have modified your shell configuration, start a new shell to initialize `rbenv`.
+
+5. Install a current stable ruby version
+  ```
+  # install and set up v3.1.3 of Ruby
+  rbenv install 3.1.3 && rbenv rehash
+  ```
+
+6. Activate your ruby version. Here you have a few options:
+
+   a. If you want to set the global ruby version that will be used wherever you use `ruby`, you can use
+   ```
+   rbenv global 3.1.3
+   ```
+
+   b. To only use this version of ruby within the repository only, navigate to the root of this repository and use:
+   ```
+   rbenv local 3.1.3
+   ```
+   This will create a `.ruby-version` file that will automatically activate this version of ruby whenever you are in this directory.
+
+7. Now you should be ready to install Bundler:
+```
+gem install bundler
+```
+
+8. Finally, run `bundle install` from the root of this repository, where the `Gemfile` is located.
+This will install all additional dependencies.
+
+### Running a local jekyll server
+
+Once all dependencies are installed, you should be able to start a local jekyll server with:
+
+```
+bundle exec jekyll serve
+```
 
-Please find the workshop website at: https://alexslemonade.github.io/2024-june-training/