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‎vignettes/howto.Rmd renamed to ‎HOWTO_BUILD_WORKSHOP.md

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---
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title: "How to Create a Workshop Package"
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subtitle: "(Automatically)"
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author: Sean Davis^[[email protected]]
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{How to create a workshop package}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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## Quickstart
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- [ ] Clone this repo (not fork)
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- [ ] Clone this repo, fork and rename it, or create a repo from this template
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- [ ] Edit `DESCRIPTION` file
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- [ ] Change package name
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- [ ] Change title and description
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### Edit `.github/workflows/basic_checks.yaml`
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**You MUST change the `repository` line in this yaml file to be YOUR
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desired Docker image name**. In other words, this section of the github
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actions file will build and push to dockerhub the image with this name.
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```yaml
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- uses: docker/build-push-action@v1
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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# change the next line to reflect the name
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# of YOUR dockerhub repository
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repository: seandavi/buildabiocworkshop2020
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tag_with_ref: true
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tag_with_sha: true
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tags: latest
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```
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### Add "secrets" to github repo
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- required secrets and their names
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- `DOCKER_USERNAME`
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- `DOCKER_PASSWORD`
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- `
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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- Github `ACCESS_TOKEN`
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‎README.md

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# Workshop Title
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## BuildABiocWorkshop2020
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Authors:
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Author Name^[Institution],
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Another Author^[Another Institution].
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<br/>
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Last modified: 14 May, 2018.
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This package is a template for building a Bioconductor 2020 workshop. The package
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includes Github actions to:
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## Overview
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1. Set up bioconductor/bioconductor_docker:devel on Github resources
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2. Install package dependencies for your package (based on the `DESCRIPTION` file)
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3. Run `rcmdcheck::rcmdcheck`
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4. Build a pkgdown website and push it to github pages
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5. Build a docker image with the installed package and dependencies
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### Description
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## Results of successful deployment
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Along with the topic of your workshop, include how students can expect
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to spend their time. For the description may also include information
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about what type of workshop it is (e.g. instructor-led live demo, lab,
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lecture + lab, etc.). Instructors are strongly recommended to provide
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completely worked examples for lab sessions, and a set of stand-alone
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notes that can be read and understood outside of the workshop.
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- A working docker image that contains the installed package and dependencies.
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- An up-to-date `pkgdown` website at https://YOURUSERNAME.github.io/YOURREPOSITORYNAME/
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- Docker image will be tagged with `latest`, `sha-XXXXXX` where `XXXXXX` is the hash of the current `master` commit, and `master`.
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### Pre-requisites
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## To use the resulting image:
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List any workshop prerequisites, for example:
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```sh
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docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME
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```
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Once running, navigate to https://localhost:8787/ and then login with `rstudio`:`yourchosenpassword`.
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* Basic knowledge of R syntax
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* Familiarity with the GenomicRanges class
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* Familiarity with xyz vignette (provide link)
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To try with **this** repository docker image:
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List relevant background reading for the workshop, including any
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theoretical background you expect students to have.
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```sh
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docker run -e PASSWORD=abc -p 8787:8787 seandavi/buildabiocworkshop2020
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```
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* List any textbooks, papers, or other reading that students should be
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familiar with. Include direct links where possible.
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### Participation
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## Details
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Describe how students will be expected to participate in the workshop.
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For detailed instructions, see [HOWTO_BUILD_WORKSHOP.md].
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### _R_ / _Bioconductor_ packages used
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## Whatcha get
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List any _R_ / _Bioconductor_ packages that will be explicitly covered.
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### Time outline
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An example for a 45-minute workshop:
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| Activity | Time |
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|------------------------------|------|
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| Packages | 15m |
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| Package Development | 15m |
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| Contributing to Bioconductor | 5m |
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| Best Practices | 10m |
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### Workshop goals and objectives
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List "big picture" student-centered workshop goals and learning
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objectives. Learning goals and objectives are related, but not the
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same thing. These goals and objectives will help some people to decide
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whether to attend the conference for training purposes, so please make
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these as precise and accurate as possible.
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*Learning goals* are high-level descriptions of what
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participants will learn and be able to do after the workshop is
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over. *Learning objectives*, on the other hand, describe in very
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specific and measurable terms specific skills or knowledge
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attained. The [Bloom's Taxonomy](#bloom) may be a useful framework
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for defining and describing your goals and objectives, although there
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are others.
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### Learning goals
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Some examples:
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* describe how to...
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* identify methods for...
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* understand the difference between...
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### Learning objectives
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* analyze xyz data to produce...
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* create xyz plots
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* evaluate xyz data for artifacts
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## Workshop
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Divide the workshop into sections (`## A Section`). Include
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fully-evaluated _R_ code chunks. Develop exercises and solutions, and
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anticipate that your audience will walk through the code with you, or
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work on the code idependently -- do not be too ambitious in the
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material that you present.
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![dockerhub](inst/images/dockerhub.png)

‎inst/images/dockerhub_result.png

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‎vignettes/workshop_example.Rmd

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---
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title: "An Example Workshop"
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author: Sean Davis^[[email protected]]
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{An Example Workshop}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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# Workshop Title
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Authors:
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Author Name^[Institution],
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Another Author^[Another Institution].
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<br/>
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Last modified: 14 May, 2018.
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## Overview
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29+
### Description
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Along with the topic of your workshop, include how students can expect
32+
to spend their time. For the description may also include information
33+
about what type of workshop it is (e.g. instructor-led live demo, lab,
34+
lecture + lab, etc.). Instructors are strongly recommended to provide
35+
completely worked examples for lab sessions, and a set of stand-alone
36+
notes that can be read and understood outside of the workshop.
37+
38+
### Pre-requisites
39+
40+
List any workshop prerequisites, for example:
41+
42+
* Basic knowledge of R syntax
43+
* Familiarity with the GenomicRanges class
44+
* Familiarity with xyz vignette (provide link)
45+
46+
List relevant background reading for the workshop, including any
47+
theoretical background you expect students to have.
48+
49+
* List any textbooks, papers, or other reading that students should be
50+
familiar with. Include direct links where possible.
51+
52+
### Participation
53+
54+
Describe how students will be expected to participate in the workshop.
55+
56+
### _R_ / _Bioconductor_ packages used
57+
58+
List any _R_ / _Bioconductor_ packages that will be explicitly covered.
59+
60+
### Time outline
61+
62+
An example for a 45-minute workshop:
63+
64+
| Activity | Time |
65+
|------------------------------|------|
66+
| Packages | 15m |
67+
| Package Development | 15m |
68+
| Contributing to Bioconductor | 5m |
69+
| Best Practices | 10m |
70+
71+
### Workshop goals and objectives
72+
73+
List "big picture" student-centered workshop goals and learning
74+
objectives. Learning goals and objectives are related, but not the
75+
same thing. These goals and objectives will help some people to decide
76+
whether to attend the conference for training purposes, so please make
77+
these as precise and accurate as possible.
78+
79+
*Learning goals* are high-level descriptions of what
80+
participants will learn and be able to do after the workshop is
81+
over. *Learning objectives*, on the other hand, describe in very
82+
specific and measurable terms specific skills or knowledge
83+
attained. The [Bloom's Taxonomy](#bloom) may be a useful framework
84+
for defining and describing your goals and objectives, although there
85+
are others.
86+
87+
### Learning goals
88+
89+
Some examples:
90+
91+
* describe how to...
92+
* identify methods for...
93+
* understand the difference between...
94+
95+
### Learning objectives
96+
97+
* analyze xyz data to produce...
98+
* create xyz plots
99+
* evaluate xyz data for artifacts
100+
101+
## Workshop
102+
103+
Divide the workshop into sections (`## A Section`). Include
104+
fully-evaluated _R_ code chunks. Develop exercises and solutions, and
105+
anticipate that your audience will walk through the code with you, or
106+
work on the code idependently -- do not be too ambitious in the
107+
material that you present.
108+
109+
110+

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