This repository contains details of the build process and usage for materials from the Bioc2019 conference.
https://rebrand.ly/biocworkshops2019
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:
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:
.travis.yml
for Continuous Integration against bioc-devel.inst/vignettes
and reference them
in the vignette using system.file
build_vignettes=TRUE
when building the package.#
), 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.BiocStyle
functionality. The style will be based on bookdown/gitbook.Update the DESCRIPTION file adding packages utilized in your workshop to the Imports field.
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.
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
This work is licensed under a Creative Commons Attribution 4.0 International License.