Initial commit

.github/ISSUE_TEMPLATE/course-content-add.md

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+---
+name: New content idea
+about: Suggest an idea for the course
+title: ''
+labels: ''
+assignees:
+
+---
+
+## Describe the your scope of your content idea
+<!-- What will this cover and how does it relate to the current course material? -->
+
+## Describe the learning objectives for your content idea
+<!-- What will users learn from this new content? -->
+
+## Additional context or resources
+<!-- Add any other context or related resources we should know about? -->

.github/ISSUE_TEMPLATE/course-problem-report.md

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+---
+name: Course Problem Report
+about: Create a report to help improve the course
+title: [Problem]
+labels: bug
+assignees:
+
+---
+
+## Describe what is not working with the course
+<!-- A clear and concise description of what the bug is. -->
+
+## Steps to Reproduce
+<!-- Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+-->
+
+## Expected behavior
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Screenshots
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## Additional context
+<!-- Add any other context about the problem here. -->

.github/PULL_REQUEST_TEMPLATE.md

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+<!--This PR Template was modified from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/.github/PULL_REQUEST_TEMPLATE.md-->
+
+### Purpose/implementation Section
+
+#### What changes are being implemented in this Pull Request?
+
+
+
+#### What was your approach?
+
+
+
+#### What GitHub issue does your pull request address?
+
+
+
+### Tell potential reviewers what kind of feedback you are soliciting.
+
+
+
+### New Content Checklist
+
+- [ ] New content/chapter is in an Rmd file with [this kind of format and headers](https://github.com/jhudsl/OTTR_Template/blob/main/02-chapter_of_course.Rmd).
+
+- [ ] New content/chapter contains [Learning Objectives and are in the correct format](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#learning-objectives-formatting).
+
+- [ ] [Bookdown successfully re-renders and any new content files have been added to the _bookdown.yml](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-with-Bookdown).
+
+- [ ] Spell check runs successfully in [Github actions style-n-check](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#spell-check)).
+
+- [ ] Any newly necessary packages that are needed have been added to the [Dockerfile and image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#adding-packages-to-the-dockerfile).
+
+- [ ] Images are in the [correct format for rendering](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text).
+
+- [ ] Every new image has [alt text and is in a Google Slide](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#accessibility).
+
+- [ ] Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this.
+
+- [ ] The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies.
+You can check this using [Color Oracle](https://colororacle.org/).

.github/automatic-issues/add-feedback-method.md

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+
+To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through.
+
+A feedback method (Google Form) has already been provided for AnVIL and GDSCN courses. Github actions automatically populates the Google Form with the `title` field from [`index.Rmd`](https://github.com/jhudsl/AnVIL_Template/blob/main/index.Rmd) using the [AnVIL Feedback Script](https://github.com/jhudsl/AnVIL_Template/blob/main/scripts/AnVIL_Feedback_Script.sh).
+
+- [ ] The `title` field has been filled out in the header yaml of `index.Rmd`.
+
+*No further action is needed on your part*. However, if you would like to change the feedback method, you can do so by editing [this line of code](https://github.com/jhudsl/AnVIL_Template/blob/7c501e9804cf88a151832bb0a9bbc1eae9d23fdf/_output.yml#L19) in `_output.yml`.
+
+[See these instructions](https://docs.google.com/document/d/1uhGafEkbtJL3ar3TVHqRFypwTbXjudHa7h2mXu53CkA/edit?usp=sharing) for how to manually create a feedback link for AnVIL / GDSCN content or events.

.github/automatic-issues/add-repo-to-anvil-collection.md

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+
+If you want this repository to be added to the AnVIL Collection, make sure you do the following:
+
+- Click the gear icon on the top right of the "Code" page next to "About"
+- [ ] Create a repository description
+- [ ] Add the homepage where your course will be rendered
+- [ ] Add a description of your course/content
+- [ ] Add the topic tag `anvil` or `gdscn`. You should also supply any other relevant tags.
+
+Following these steps will also automatically add this repository to the [AnVIL Collection](https://hutchdatascience.org/AnVIL_Collection/) if this repository is owned by one of the DaSL organizations.
+
+For more information on these settings see instructions in the [wiki pages](https://github.com/jhudsl/AnVIL_Template/wiki/The-AnVIL-Collection#adding-your-course-to-the-anvil-collection).
+
+For more information about adding repositories to the DaSL Collection, see the [AnVIL Collection README](https://github.com/fhdsl/AnVIL_Collection#readme).

.github/automatic-issues/git-secrets.md

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+
+**Note these steps are only pertinent if you are setting up this course outside of the jhudsl organization**
+
+For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-GitHub-secrets).
+
+It's important that these are set up and named exactly what they are below in order for Github actions to work correctly.
+
+To set up these repository secrets, on your repository's main Github page, go to `Settings` and scroll down to see `Secrets` on the left side menu bar.
+
+- [ ] Set `GH_PAT`
+`Name`:  `GH_PAT`
+`value`: A personal access token [following these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token).
+Underneath `Select scopes`, check both `repo` and `workflow`.
+Then copy the PAT and save as the value.

.github/automatic-issues/images-checklist.md

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+
+Use this checklist to make sure your slides and images are set up correctly!
+
+See [Setting Up Images and Graphics](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics) for more info!
+
+- [ ] Create your [course's main Google Slides](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics)
+
+- [ ] The slides use the [appropriate template](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics).
+
+- [ ] Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this.
+
+- [ ] The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies.
+You can check this using [Color Oracle](https://colororacle.org/).
+
+- [ ] Every image is [inserted into the text](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text) using one of these options: `ottrpal::include_slide()`, `knitr::include_image()`, or this format: `<img src="blah.png" alt="SOMETHING">`.
+
+- [ ] Every image has [alternative text added to it](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text).
+
+- [ ] The beginning of each Rmd contains this chunk so the images are saved in the correct spot:
+
+`````
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+`````

.github/automatic-issues/set-repo-settings.md

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+
+For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course).
+
+- [ ] This course repository is set to `public`.
+- [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings#add-jhudsl-robot-as-a-collaborator).
+- [ ] [GH_PAT has been set up as a GitHub secret](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token)
+
+- [ ] GitHub pages is turned on
+  - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`.  
+  - [ ] Check `Enforce HTTPS`.
+
+- [ ] [Github secret `GH_PAT` has been set](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token)
+  `Name`:  `GH_PAT`
+  `value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+  Underneath `Select scopes`, check both `repo` and `workflow`.
+  Then copy the PAT and save as the value.
+
+- [ ] [Set branch protections settings](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#9-set-up-branch-rules)
+  - [ ] `main` branch has been set up:
+    - [ ] `Require pull request reviews before merging` box is checked.
+    - [ ] `Require status checks to pass before merging` box is checked.
+      - [ ] Underneath that `Require branches to be up to date before merging` box is checked.
+  - [ ] Click `Save` at the bottom of the page!
+
+- [ ] [Customize GitHub actions](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots) for what you will need in this course.

.github/automatic-issues/templates-to-edit.md

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+
+[Follow the Wiki instructions here](https://github.com/jhudsl/OTTR_Template/wiki/Start-editing-your-course) for details on how to complete the items in this issue.
+
+The following files need to be edited to get this new course started!
+
+### Files that need edited upon creating a new course.
+
+- [ ] `README.md` - Fill in all the `{ }`.
+- [ ] `index.Rmd` - `title:` should be updated.
+- [ ] `01-intro.Rmd` - replace the information there with information pertinent to this new course.
+- [ ] `02-chapter_of_course.Rmd` - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted.
+
+### Files that need to be edited upon adding each new chapter (including upon creating a new course):
+
+- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-with-Bookdown).
+- [ ] `book.bib` - any citations need to be added. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Citations).
+
+### Picking a style
+
+See more [about customizing style on this page in the guide](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style).
+By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.
+
+#### Using a style set
+
+[Read more about the style sets here](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style#using-a-style-set).
+
+- [ ] On a new branch, copy the `style-sets/<set-name>/index.Rmd` and `style-sets/<set-name>/_output.yml` to the top of the repository to overwrite the default `index.Rmd` and `_output.yml`.
+- [ ] Copy over all the files in the `style-sets/<set-name>/copy-to-assets` to the `assets` folder in the top of the repository.
+- [ ] [Create a pull request](https://github.com/jhudsl/OTTR_Template/wiki/Start-editing-your-course#getting-started-with-the-github-workflow) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
+
+### Files that need to be edited upon adding new packages that the book's code uses:
+
+- `docker/Dockerfile` needs to have the new package added so it will be installed. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image).
+- The code chunk in `index.Rmd` should be edited to add the new package.

.github/automatic-issues/update-enrollment.md

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+
+The original template: https://github.com/jhudsl/OTTR_Template is always a work in progress.
+We are working on adding more features and smoothing out bugs as we go. The AnVIL Template collects these and can pass them along to this repository.
+
+If you want to receive updates from the AnVIL template to your course template, you will need to enroll this repository to the template updates by adding it to the `sync.yml` file.
+
+- [ ] [Follow these instructions](https://github.com/jhudsl/AnVIL_Template/wiki/Start-a-New-Book-or-Course#enroll-your-repository-for-anvil-updates) to enroll your course repository to receive these updates.
+
+- [ ] [Ensure that you have followed these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#5-add-jhudsl-robot-as-a-collaborator) to add the `jhudsl-robot` as a collaborator to your repository.

.github/switch_sync_repo.R

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+#!/usr/bin/env Rscript
+
+# This script switches the repo entry for the yaml file to whatever is specified
+# Written by Candace Savonen Jan 2022
+
+if (!("optparse" %in% installed.packages())){
+  install.packages("optparse")
+}
+
+library(optparse)
+
+option_list <- list(
+  optparse::make_option(
+    c("--repo"),
+    type = "character",
+    default = "jhudsl/OTTR_Template_Test",
+    help = "GitHub repository name, e.g. jhudsl/OTTR_Template_Test",
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Get test sync yaml path
+sync_file_path <- file.path(root_dir, ".github", "test-sync.yml")
+
+yaml_contents <- yaml::yaml.load_file(sync_file_path)
+
+# Only keep first grouping
+yaml_contents$group <- yaml_contents$group[[1]]
+
+# Switch out repo
+yaml_contents$group$repos <- opt$repo
+
+yaml::write_yaml(yaml_contents, sync_file_path)

.github/sync.yml

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+# For info on how to update this file see: https://github.com/marketplace/actions/repo-file-sync-action#%EF%B8%8F-sync-configuration
+
+group:
+  - files:
+      - source: .github/workflows/
+        dest: .github/workflows/
+        exclude: |
+          send-updates.yml
+          test-send-updates.yml
+          starting-course.yml
+          release-notes.yml
+      - source: .github/ISSUE_TEMPLATE/course-problem-report.md
+        dest: .github/ISSUE_TEMPLATE/course-problem-report.md
+      - source: .github/ISSUE_TEMPLATE/course-content-add.md
+        dest: .github/ISSUE_TEMPLATE/course-content-add.md
+      - source: scripts/ottr-fy.R
+        dest: scripts/ottr-fy.R
+      - source: scripts/git_repo_check.R
+        dest: scripts/git_repo_check.R
+      - source: scripts/make_screenshots.R
+        dest: scripts/make_screenshots.R
+      - source: scripts/AnVIL_Feedback_Script.sh
+        dest: scripts/AnVIL_Feedback_Script.sh
+      - source: code_of_conduct.md
+        dest: code_of_conduct.md
+      - source: style-sets
+        dest: style-sets
+      - source: assets/box_images/
+        dest: assets/box_images/
+      - source: assets/AnVIL_style/
+        dest: assets/AnVIL_style/
+        deleteOrphaned: true
+      - source: assets/GDSCN_style/
+        dest: assets/GDSCN_style/
+        deleteOrphaned: true
+      - source: assets/itcr_arrow.png
+        dest: assets/itcr_arrow.png
+      - source: assets/style.css
+        dest: assets/style.css
+      - source: assets/toc_close.css
+        dest: assets/toc_close.css
+  # Repositories to receive changes
+    repos: |
+      fhdsl/AnVIL_Book_Epigenetics_Intro
+      fhdsl/AnVIL_Demos
+      fhdsl/AnVIL_Outreach_Dashboard
+      fhdsl/AnVIL_SRA_Data
+      fhdsl/AnVIL_Urban_Genomics_PCA
+      fhdsl/GDSCN_BioDIGS_AMR
+      fhdsl/GDSCN_BioDIGS_Book
+      fhdsl/GDSCN_BioDIGS_Soil
+      fhdsl/GDSCN_SARS_RStudio_on_AnVIL
+      jhudsl/AnVIL_Book_Getting_Started
+      jhudsl/AnVIL_Book_Instructor_Guide
+      jhudsl/AnVIL_Book_WDL
+      jhudsl/AnVIL_Book_WDL
+      jhudsl/AnVIL_Phylogenetic-Techniques
+      jhudsl/GDSCN_Book_SARS_Galaxy_on_AnVIL
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_Differential_Expression
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_PCA
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_RNA-seq
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq
+      jhudsl/GDSCN_Book_swirl
+###ADD NEW REPO HERE following the format above#
+
+# AnVIL repos should sync AnVIL version of _output.yml
+  - files:
+      - source: _output.yml
+        dest: _output.yml
+    repos: |
+      fhdsl/AnVIL_Book_Epigenetics_Intro
+      fhdsl/AnVIL_Collection
+      fhdsl/AnVIL_Data_Subsetting
+      fhdsl/AnVIL_Demos
+      fhdsl/AnVIL_Outreach_Dashboard
+      fhdsl/AnVIL_Researcher_Journey
+      fhdsl/AnVIL_SRA_Data
+      fhdsl/AnVIL_Urban_Genomics_PCA
+      jhudsl/AnVIL_Book_WDL
+
+# GDSCN repos should sync the GDSCN version of _output.yml
+# They should also sync the top level assets into an AnVIL style-set
+  - files:
+      - source: style-sets/GDSCN/_output.yml
+        dest: _output.yml
+      - source: _output.yml
+        dest: style-sets/AnVIL/_output.yml
+      - source: index.Rmd
+        dest: style-sets/AnVIL/index.Rmd
+    repos: |
+      fhdsl/GDSCN_BioDIGS_AMR
+      fhdsl/GDSCN_BioDIGS_Book
+      fhdsl/GDSCN_BioDIGS_Soil
+      fhdsl/GDSCN_SARS_RStudio_on_AnVIL
+      jhudsl/GDSCN_Template_Test
+
+# Repos where Hopkins took the lead have JHU branding instead of Hutch
+  - files:
+      - source: style-sets/AnVIL_JHU/_output.yml
+        dest: _output.yml
+      - source: _output.yml
+        dest: style-sets/AnVIL/_output.yml
+      - source: index.Rmd
+        dest: style-sets/AnVIL/index.Rmd
+    repos: |
+      jhudsl/AnVIL_Book_Getting_Started
+      jhudsl/AnVIL_Book_Instructor_Guide
+      jhudsl/AnVIL_Book_WDL
+      jhudsl/AnVIL_Phylogenetic-Techniques
+
+  - files:
+      - source: style-sets/GDSCN_JHU/_output.yml
+        dest: _output.yml
+      - source: _output.yml
+        dest: style-sets/AnVIL/_output.yml
+      - source: index.Rmd
+        dest: style-sets/AnVIL/index.Rmd
+    repos: |
+      jhudsl/GDSCN_Book_SARS_Galaxy_on_AnVIL
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_Differential_Expression
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_PCA
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_RNA-seq
+      jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq
+      jhudsl/GDSCN_Book_swirl
+
+