This repository contains details of the build process and usage for materials from the Bioc2019 conference.

Compiled Workshops Link

https://rebrand.ly/biocworkshops2019

Running workshop materials locally

The workshops (except the CWL workshop) are all installed and ready-to-run inside docker; you will need to install docker on your machine to follow along. We have a base docker image seandavi/bioc_2019 that contains the operating system and base R installation. The workshops and additional package (over 600) are included as a separate download that can be mounted into the container as a volume. To use the entire set of workshop materials, do:

• Make a directory for the installed packages:

  mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space
  

• Download and untar entire tar.gz file with all installed packages and materials:

  cd /home/ubuntu/bioc-libs # use the directory from above
  wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
  tar -xzf bioc2019-usr-local.tar.gz
  

• Run docker locally with (you may or may not need sudo depending on your docker setup):

  # again, use the directory from above
  sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
      -p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019
  

• Credentials:

  • username: 'rstudio'
  • password: 'as you set it--bioc above'

Instructions For Workshop Authors

Getting started

To contribute a new workshop, open a BiocWorkshops issue starting with the [Workshop] keyword in the title of the issue. Provide a link to the repository in the issue message body. You may also include GitHub usernames of workshop collaborators. For a successful workshop build, adhere to the following:

1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
2. Include a standard vignette in the vignettes directory
3. Put any extra files (images, .bib) in inst/vignettes and reference them in the vignette using system.file
4. Number 3 requires package chapter installation before vignette build or build_vignettes=TRUE when building the package.
5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.

DESCRIPTION

Update the DESCRIPTION file adding packages utilized in your workshop to the Imports field.

Use bioc-devel

BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.

Deadlines for Bioc2019

Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York

• Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
• Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
• Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.

This work is licensed under a Creative Commons Attribution 4.0 International License.