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TEST_Workshop.md

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Testing your Bioconductor Workshop on Travis CI

Please refer to this website for detailed instructions on setting up Travis to build your Bioconductor Workshop chapter: https://bookdown.org/yihui/bookdown/github.html

Be sure to enable Travis for your fork of the workshops repository by going to: https://www.travis-ci.org/account/repositories and moving the slider to the right.

GitHub Personal Access Token

In order to set up Travis, you will need a GitHub PAT. You can generate one via the usethis package:

library(usethis)

## Check to see if a PAT exists already:
github_token()

## If it doesn't, run this and follow instructions:
browse_github_token()

You will then need to save the environment variable via Travis in your repository's settings by going to the Travis CI website page for your project.

Creating a gh-pages branch

To build your chapter, you will need to create a GitHub Pages branch. You can use the following commands to checkout the branch and to clear the current directory in the branch:

git checkout --orphan gh-pages
git rm -rf .

# create a hidden file .nojekyll
touch .nojekyll
git add .nojekyll

Then commit the branch to GitHub:

git commit -m "Initial commit"
git push origin gh-pages

Files to include in your repository

To build your book / chapter, you will need a few files:

  • _bookdown.yml
  • .travis.yml
  • _build.sh
  • _deploy.sh
  • DESCRIPTION

See the templates in the BiocWorkshops2019 folder.