Update setup text handling

components/dictionary.txt

@@ -103,7 +103,7 @@ macOS
 MAF
 md
 medulloblastoma
-Miniconda
+Miniforge
 Monterey
 multifactor
 Muris
@@ -112,6 +112,7 @@ natively
 Nextflow
 nonconsensual
 Nüst
+openrrp
 OpenScPCA
 OpenScPCA's
 ord

docs/HOME.md

@@ -12,13 +12,16 @@ The <b><a href="https://www.ccdatalab.org/" title="Alex's Lemonade Stand Foundat
 The Childhood Cancer Data Lab is an initiative of <b><a href="https://www.alexslemonade.org/" title="Alex's Lemonade Stand Foundation">Alex's Lemonade Stand Foundation</a></b>.
 </p>
 
-**Workshop day one - May 14:** 
 We will introduce concepts in reproducible computational research for genomics, including tools and approaches for organizing, managing, and sharing your code.
 
-**Workshop day two (optional) - May 15:** 
-Participants can choose to continue the workshop and learn how to put their skills to use for the [Open Single-cell Pediatric Cancer Atlas (OpenScPCA)](https://openscpca.readthedocs.io/en/latest/), a pediatric cancer research project organized by the Data Lab. 
+<!-- These sentences will only appear if the workshop is OpenRRP.-->
+{% if site.include_openrrp %}
+
+Participants can choose to continue the workshop and learn how to put their skills to use for the [Open Single-cell Pediatric Cancer Atlas (OpenScPCA)](https://openscpca.readthedocs.io/en/latest/), a pediatric cancer research project organized by the Data Lab.
 We will teach you how to contribute and we'll get you completely set up so you can dive right into analysis as soon as the workshop ends!
 
+{% endif %}
+
 Before the workshop starts, be sure to visit our [Pre-workshop Setup page](setup_instructions/setup_overview.md) for instructions on preparing your computer for the workshop.
 _Completing these setup steps is **required** for full participation in the hands-on activities._
 
@@ -27,5 +30,5 @@ Please also review our [Code of Conduct](code-of-conduct.md).
 You will also want to review the [Participant Information](participant_information.md) page for details about the workshop location and other logistics.
 
 
-**Looking for more?** 
+**Looking for more?**
 We have compiled a set of [useful resources](reproducibility_resources.md) that support reproducible computational research that we recommend for your future reading and exploration!

docs/_config.yaml

@@ -13,5 +13,5 @@ header_pages:
   - setup_instructions/setup_overview.md
   - workshop-schedule.md
 
-
-
+# Whether or not OpenRRP information and setup instructions should be included
+include_openrrp: false

docs/setup_instructions/openrrp-setup.md

@@ -0,0 +1,29 @@
+
+
+## Also staying for the OpenScPCA portion of the workshop?
+
+If you are staying for the optional component of the workshop to learn about the OpenScPCA project, there are a few more setup steps you will need to follow.
+These instructions are based on the full [OpenScPCA Project's setup instructions](https://openscpca.readthedocs.io/en/latest/technical-setup/), but you only need to follow the specific steps listed here.
+
+1. Before the workshop, you will receive an email inviting you to join AWS IAM Identity Center, which will allow you to access OpenScPCA data and compute resources.
+    - [Follow these instructions](https://openscpca.readthedocs.io/en/latest/aws/joining-aws/) to accept this invitation and configure multifactor authentication.
+    - _You are only eligible for an OpenScPCA AWS account after you fill out the [OpenScPCA intake form](https://share.hsforms.com/1MlLtkGYSQa6j23HY_0fKaw336z0) where you agree to [OpenScPCA's policies](https://openscpca.readthedocs.io/en/latest/policies/)._
+
+2. [Install Miniforge](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-conda/#install-conda), a lightweight distribution of the package management software conda.
+    - If you are on a Windows machine, will need to install Miniforge into the WSL 2 (Ubuntu) side of your computer
+    - You do _not_ need to also set up conda; we will do this together during the workshop
+
+### Additional installations for Windows users
+
+Previously, you should have [already installed R/RStudio, Visual Studio Code, and GitKraken](windows_installation_instructions.html) onto the _Windows_ side of your computer.
+
+You will now need to perform some additional installations that let you use these platforms from the WSL 2 (Ubuntu) side of your computer, either by installing a new version of the software or a software plugin.
+
+Now, you will need to install install softwares again, but onto the WSL 2 (Ubuntu) side of your computer, as well as other programming tools.
+Follow these instructions to complete the additional installations:
+
+1. [Install GitKraken](https://openscpca.readthedocs.io/en/latest/technical-setup/install-a-git-client/#install-gitkraken-on-windows-with-wsl-2) onto the WSL 2 (Ubuntu) side of your computer
+    - You should also authenticate this version of GitKraken with your GitHub account
+2. [Install R](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/install-r-rstudio/#install-r-on-windows-with-wsl-2) onto the WSL 2 (Ubuntu) side of your computer
+3. [Install RStudio Server](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/install-r-rstudio/#install-rstudio-server-on-windows-with-wsl-2) onto the WSL 2 (Ubuntu) side of your computer
+4. To enable you to use Visual Studio Code from Ubuntu, [install the WSL 2 extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsld)

docs/setup_instructions/setup_overview.md

@@ -3,87 +3,38 @@ title: Pre-workshop setup
 nav_title: Setup
 ---
 
-This will be a hands-on workshop, so to maximize our time, we would like you to arrive having completed a number of setup tasks, namely installing software that we will be using.
-We will _not_ have time to do all of the setup on the day of the workshop and accomplish all of our goals for the workshop!
-
-## Set up your accounts
-
-Before the workshop begins, you will need to create and configure your GitHub account.
-You will also need to set up your OpenScPCA Amazon Web Services (AWS) account.
-
-1. [Create a GitHub account](./github_gitkraken_setup_instructions.md#creating-a-github-account) if you do not already have one.
-    - You should also [turn on two-factor authentication (2FA)](./github_gitkraken_setup_instructions.md#enabling-two-factor-authentication-2fa-on-github) after you create your account.
-
-2. Before the workshop, you will receive an email inviting you to join AWS IAM Identity Center, which will allow you to access OpenScPCA data and compute resources.
-    - [Follow these instructions](https://openscpca.readthedocs.io/en/latest/software-platforms/aws/joining-aws/) to accept this invitation and configure multifactor authentication.
-    - _You are only eligible for an OpenScPCA AWS account after you fill out the [OpenScPCA intake form](https://share.hsforms.com/1MlLtkGYSQa6j23HY_0fKaw336z0) where you agree to [OpenScPCA's policies](https://openscpca.readthedocs.io/en/latest/policies/)._
-
-## Workshop software installations
-
-You will also need to set up your computers following _some_ these software installation steps in the [OpenScPCA Project's setup instructions](https://openscpca.readthedocs.io/en/latest/technical-setup/), as detailed below.
-
-You should not complete all setup steps on the OpenScPCA website, since we will be doing some steps together as part of the workshop itself, but you should come prepared with all software installed and ready to be further set up.
-
-## Instructions for macOS users
-
-1. [Install GitKraken](https://openscpca.readthedocs.io/en/latest/technical-setup/install-a-git-client/#install-gitkraken), a GUI for working with Git
-    - Follow the instructions in the link above to also sign into GitKraken with your GitHub account
-    - [See these instructions](./github_gitkraken_setup_instructions.md#setting-up-gitkraken) for additional information about setting up GitKraken
-2. [Install Miniconda](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-conda/#install-conda), a lightweight distribution of the package management software conda
-    - You do _not_ need to also set up conda; we will do this together during the workshop
-3. [Install R and RStudio](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/install-r-rstudio/#install-r-on-macos)
-    - Follow the instructions to install the additional tools (XCode develop tools and the GNU Fortran compiler) as well.
-4. Install some R packages we will use in the workshop by running the following command in R Console:
-    ```r
-    install.packages(c("renv", "tidyverse", "rmarkdown", "here", "optparse"))
-    ```
-5. Install [Visual Studio Code (VS Code)](https://code.visualstudio.com/), a popular text editor
-    - If you prefer to use a different text editor, that's fine!
-    But, we do _not_ recommend using Mac's native TextEdit application.
+This will be a hands-on workshop, so to maximize our time, we would like you to arrive having completed a number of setup tasks, namely setting up accounts and installing software that we will be using.
 
+We will _not_ have time to do all of the setup on the day of the workshop and accomplish all of our goals for the workshop!
+Please be aware this setup process may take 1-2 hours to complete if you are using Windows, and somewhat less on a Mac.
 
-## Instructions for Windows users
-
-OpenScPCA currently only supports development on macOS or Linux.
-Therefore, you will need to install and set up for development using the Windows Subsystem for Linux, which provides you with a natively-running Ubuntu operating system on your Windows computer.
-
-For most of the installations below (all except Visual Studio Code), you will install software directly into the WSL 2 side of your computer, _not_ the Windows side.
-Even if you already have any of these softwares installed on the Windows side of your computer, you still need to install them on the WSL 2 side as described below.
-
-
-1. Install [Windows Subsystem for Linux 2](https://openscpca.readthedocs.io/en/latest/technical-setup/install-wsl-2/)
-    - Follow all instructions in the link above to install WSL 2, create your Ubuntu account, and update `apt`
-2. [Install GitKraken](https://openscpca.readthedocs.io/en/latest/technical-setup/install-a-git-client/#install-gitkraken-on-windows-with-wsl-2) into the WSL 2 side of your computer
-    - Follow the instructions in the link above to also sign into GitKraken with your GitHub account
-3. [Install Miniconda](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-conda/#install-conda), a lightweight distribution of the package management software conda, into the WSL 2 side of your computer
-    - You do _not_ need to also set up conda; we will do this together during the workshop
-4. [Install R and RStudio Server](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/install-r-rstudio/) into the WSL 2 side of your computer
-5. Install some R packages we will use in the workshop by running the following command in R Console:
-    ```r
-    install.packages(c("renv", "tidyverse", "rmarkdown", "here", "optparse"))
-    ```
-6. Install [Visual Studio Code (VS Code)](https://code.visualstudio.com/), a popular text editor, into the Windows side of your computer
-    - [Following these instructions](https://code.visualstudio.com/docs/remote/wsl#_getting-started), you should also install and turn on the [WSL 2 extension](https://code.visualstudio.com/docs/remote/wsl#_getting-started) to be able to use VS Code from WSL 2
-
+If you need any assistance with the installation, do not hesitate to reach out to the Data Lab team by email, or, even better, in the [Cancer Data Science Slack](http://ccdatalab.org/slack)!
+We will add you to a training-specific channel after you join the Slack community.
 
+{% if site.include_openrrp %}
+**Table of contents**
 
+* TOC goes here
+{:toc}
+{% endif %}
 
 
-<!--
+## Workshop software requirements
 
-Regular RRP installation instructions are commented out below.
+You will need to install R, RStudio, several R packages, GitKraken, and a suitable text editor, as well as any system dependencies required for these programs.
+For Windows users, you will also need to install Windows Subsystem for Linux (WSL 2).
 
-The main tasks are installation of R, RStudio, GitKraken, and a suitable text editor.
-For Windows users, we will also require the installation of Windows Subsystem for Linux (WSL).
 You may already have some of this software installed, but we encourage you to read through all of the instructions at the links below that pertain to your system.
+This is especially important for Windows users given the WSL 2 setup, which can be quite time-consuming.
+
+Please follow the instructions below for your given operating system:
 
 - [macOS installation instructions](mac_installation_instructions.md)
 - [Windows installation instructions](windows_installation_instructions.md)
 
-Finally, you will also need to create a [GitHub](https://github.com) account if you do not already have one and configure the GitKraken application.
+As part of this setup, you will also need to create a [GitHub.com](https://github.com) account if you do not already have one.
+You will also need to [configure the GitKraken application](github_gitkraken_setup_instructions.md) to interact with GitHub.
 
-- [GitHub and GitKraken setup](github_gitkraken_setup_instructions.md)
--->
-
-If you need any assistance with the installation, do not hesitate to reach out to the Data Lab team by email, or, even better, in the [Cancer Data Science Slack](http://ccdatalab.org/slack).
-We will add you to a training-specific channel after you join the Slack community.
+{% if site.include_openrrp %}
+    {% include_relative openrrp-setup.md %}
+{% endif %}

docs/setup_instructions/windows_installation_instructions.md

@@ -7,9 +7,6 @@ title: Windows Installation Instructions
 * TOC goes here
 {:toc}
 
-
-> Please be aware this setup process may take 1-2 hours to complete!
-
 ## Windows Subsystem for Linux (WSL 2)
 
 We will be using a number of UNIX-based tools throughout this workshop, and many bioinformatics packages are written for that environment.