https://github.com/bioconductor/biocworkshops2019
The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball:
https://github.com/bioconductor/biocworkshops2019
Last synced: over 1 year ago
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The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball:
- Host: GitHub
- URL: https://github.com/bioconductor/biocworkshops2019
- Owner: Bioconductor
- Created: 2019-05-03T15:00:39.000Z (about 7 years ago)
- Default Branch: devel
- Last Pushed: 2023-03-15T21:05:13.000Z (about 3 years ago)
- Last Synced: 2025-01-09T11:58:12.048Z (over 1 year ago)
- Language: Dockerfile
- Homepage: https://bioconductor.github.io/BiocWorkshops2019/
- Size: 168 MB
- Stars: 25
- Watchers: 15
- Forks: 15
- Open Issues: 34
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
This repository contains details of the build process and usage for materials
from the [Bioc2019 conference].
[Bioc2019 conference]: https://bioc2019.bioconductor.org
# 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'
[docker]: https://docker.io
[seandavi/bioc_2019]: https://cloud.docker.com/u/seandavi/repository/docker/seandavi/bioc_2019
# 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](https://bookdown.org/yihui/bookdown/usage.html) 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](https://www.bioconductor.org/developers/how-to/useDevel/) 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](https://github.com/lpantano/dummychapter1) 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.
[BiocWorkshops issue]: https://github.com/Bioconductor/BiocWorkshops2019/issues
[Bioconductor 2019 Conference]: https://bioc2019.bioconductor.org/
This work is licensed under a Creative Commons Attribution 4.0 International License.