abyzovlab/cnvpytor-course

Online Tools for Training Resources - OTTR

The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms less painful.

This template and guide helps you:

• Edit and write a course in RMarkdown files and have it published to multiple different platforms:
  • Leanpub
  • Bookdown
  • Coursera
• Have Github action robots do your repetitive tasks like spell check and re-rendering.
• Use automagic conversion to ease the lift of prepping the material for different platforms' formats.
• Use our Docker image for consistency across authors as well as to help you avoid dependency hell.

Courses that have been made using this template:

• Documentation and Usability
• Leadership for Cancer Informatics Research
• Reproducibility in Cancer Informatics
• Advanced Reproducibility in Cancer Informatics

To Get Started

• Go to the Wiki page
• Please take a look at the code of conduct.
• If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please file an issue here! Your feedback is very much appreciated.

Copy Number Analysis using CNVpytor

This course was created from this GitHub template.

You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub. Will look something like: https://jhudatascience.org/{Course_Name}}

If you would like to contribute to this course material, take a look at the getting started GitHub wiki pages.

About this course

This course introduces {info on what this course introduces}

Learning Objectives

This course will teach learners to:

• A brief Introduction to copy number analayis
• Copy number Analayis using CNVpytor

Encountering problems?

If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.

All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise.

cnvpytor-course's Issues

New Course - Set Repository Settings

For more information on these settings see instructions in the getting started GitHub wiki pages.

• This course repository is set to public.

• Add the jhudsl-robot as a collaborator to your repository..

• GH_PAT has been set up as a GitHub secret

• 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
  Name: GH_PAT
value: A personal access token following these instructions.
  Underneath Select scopes, check both repo and workflow.
  Then copy the PAT and save as the value.

• Set branch protections settings

  • 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!

Reminder - Add user feedback method

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.

See these instructions for suggestions on how to add a feedback method for this course.

New Course - Template Update Enrollment

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.

If you want to receive updates from the original 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 to enroll your course repository to receive these updates.

• Ensure that you have followed these instructions to add the jhudsl-robot as a collaborator to your repository.

New Course - Templates to Edit

Follow the Wiki instructions here 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.
• book.bib - any citations need to be added. See instructions.

Picking a style

See more about customizing style on this page in the guide.
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.

• 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 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.
• The code chunk in index.Rmd should be edited to add the new package.