https://github.com/plantinformatics/pretzel-application-note
A repository for an application note about pretzel
https://github.com/plantinformatics/pretzel-application-note
Last synced: 3 months ago
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A repository for an application note about pretzel
- Host: GitHub
- URL: https://github.com/plantinformatics/pretzel-application-note
- Owner: plantinformatics
- Created: 2018-06-20T00:16:13.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-01-11T05:22:45.000Z (over 6 years ago)
- Last Synced: 2025-01-01T04:32:07.670Z (5 months ago)
- Language: TeX
- Size: 1.55 MB
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# pretzel-application-note
A repository for an application note about [pretzel](https://github.com/plantinformatics/pretzel).
# Source
Application note is drafted in [RMarkdown](https://rmarkdown.rstudio.com/) in [`pretzel.Rmd`](pretzel.Rmd) file. RMarkdown is well intergrated in RStudio, but if you'd rather write/edit in a text editor of your choice, you can render it as per instructions below.
## Bibliography
Among the [alternatives available](https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#specifying_a_bibliography) we opted for BibTeX, see [`references.bib`](references.bib).
# Rendering
### Using docker
```sh
docker run --rm --user $(id -u):$(id -g) \
--volume $(pwd):/writing \
--workdir /writing rsuchecki/renderer:0.1 ./render.R
```
### Using singularity
Note that this is rather slow, possibly due to container conversion from docker to singularity format.
```sh
singularity exec docker://rsuchecki/renderer:0.1 ./render.R
```
### Natively
If you'd like to render the manuscript without docker/singularity, you will need the following:
* `R` e.g. on ubuntu `sudo apt apt install r-base-core`
* `pandoc` e.g. on ubuntu `sudo apt install pandoc pandoc-citeproc`
* `LaTeX` e.g. on ubuntu `sudo apt install texlive texlive-latex-extra`
* `R` packages:
* `rmarkdown`
* `rticles`
* `bookdown`
Then:
```
./render.R
```