Workflow vignettes are documents which describe a bioinformatics workflow that involves multiple Bioconductor packages. These workflows are usually more extensive than the vignettes that accompany individual Bioconductor packages.
Workflow vignettes may deal with larger data sets and/or be more computationally intensive than typical Bioconductor package vignettes. For this reason, the automated builder that produces these vignettes does not have a time limit (in contrast to the Bioconductor package building system which will time out if package building takes too long).
Anyone who is a bioinformatics domain expert.
Request that a new directory be created in our SVN repository under “/trunk/madman/workflows” and that you be given read/write access to this directory. You can request this access by emailing “maintainer at bioconductor dot org”. (You can view existing workflow sources here, username and password is readonly.)
Write a vignette in LaTeX or Markdown, using the knitr package. Commit it to the svn location above. Alternatively, you can write a full R package in this location (in this case, it’s not required to use knitr for your vignette).
Go to the DocBuilder Web App. Log in with your SVN username and password.
Click on “Create New Jenkins Project”. Fill in the directory name from the first step above, and your email address.
The workflow builder will now try and build your vignette on Mac, Windows, and Linux. You’ll receive an email if there were any errors. You can monitor the progress of builds here.
Every time you commit a change to your workflow directory, another build will be triggered and you will receive email if it fails.
When you are ready for your workflow to appear on the Bioconductor web site, contact “maintainer at bioconductor dot org” and we will allow the workflow to propagate to our web site where it will be listed alongside the other workflows. It will be updated every time there is an SVN commit and a successful build.
If you want to include math symbols in a workflow vignette, put the following snippet at the beginning of your .Rmd file:
Then you can use math the same way you would in
LaTeX, except the symbols for escaping it
are different. For inline formulae, use \\(N\\), and for displayed
equations, use $$N$$.
The first will render as \(N\) and the second as .
With a markdown vignette (.Rmd file) you can add a YAML metadata preamble at the beginning of the file, for example:
--- Author: My Name Date: March 16, 2015 ---
This metadata will be rendered in the “About This Document” box that appears at the top of the web page.
If you have any questions, please ask on the bioc-devel mailing list.