lpantano / dummychapter1

Example of package using inst files in the vignette

Instructions for the workshop development

• Clone or fork https://github.com/lpantano/dummychapter1 to use as a template for creating your workshop as an installable package
• Use vignettes/dummychapter1.Rmd vignette as a formatting example for your workshop
• Use Docker Container for Bioconductor to test your workshop for compatibility with bioconductor/bioconductor_docker:devel. This is important for attendees that will have access to Amazon Machine Images preloaded with R and RStudio servers and tested versions of all workshops. Example how to run Docker and access RStudio at http://localhost:8787/ (RStudio access works on Mac/Unix only)

docker run -e PASSWORD=bioc -p 8787:8787 -v $(pwd):/home/rstudio bioconductor/bioconductor_docker:devel

• Commit and push a sample .travis.yml file for implementing Continuous Integration against bioc-devel

  • Register on https://travis-ci.org/ with your GitHub account
  • Allow Travis access to all GitHub repositories
  • Ensure Travis sees your repository and triggers the build on push (or, change to pull request only build)

• Write your workshop vignette, modify the DESCRIPTION file to add the dependencies. It is important that all dependencies be declared and that your workshop vignette can be built without errors on the Docker image we are using.

  • Make your workshop independent on packages installable from GitHub only. We strongly recommend using packages available from CRAN or bioc-devel
  • Data should ideally come from existing Bioconductor packages or the Bioconductor ExperimentHub for speed, reliability, and local caching. If suitable data are not available via these options, additional data can be downloaded but we recommend you utilize BiocFileCache for the download process to preserve bandwidth from repeated downloading.
  • The workshops will be collated into a training booklet that will be made freely available under the CC BY 4.0 license. Review the LICENSE file - contribution of your workshop will be taken as agreement to have your workshop materials included under this license
  • Use the Build/Check button in RStudio, or R CMD check to ensure your workshop package checks without warnings

• We recommend communicating through the #biocworkshopbook channel on the community-bioc Slack team (https://community-bioc.slack.com/archives/CJDMYKG2U) for help