[Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Obenchain, Valerie Valerie.Obenchain at RoswellPark.org
Mon Dec 11 20:44:17 CET 2017


On 12/11/2017 08:49 AM, Aaron Lun wrote:

Following up on our earlier discussion:


I have split the simpleSingleCell workflow into three (four, if you
include the introductory overview) self-contained Rmarkdown files. I am
preparing them for submission to BioC's workflow builder, and I would
like to check what is the best way to do this:

i) Each workflow file goes into its own package.

ii) All workflow files go into a single package.

Option (i) is logistically easier but probably a bit odd conceptually,
especially if users need to download "simpleSingleCell1",
"simpleSingleCell2", "simpleSingleCell3", etc.

Option (ii) is nicer but requires more coordination, as the BioC webpage
builder needs to know that that multiple HTMLs have been generated. It's
also unclear to me whether this will run into problems with the DLL
limit - does R restart when compiling each vignette?

You could do either but I'd say option 2 is easier from a maintenance standpoint and probably for the user. Maybe you've seen this but an example is the annotation workflow package which houses 2 workflows:

~/repos/svn/workflows >ls annotation/vignettes/
Annotating_Genomic_Ranges.Rmd  Annotation_Resources.Rmd  databaseTypes.png  display.png

Each has an informative name and is presented on the website as an individual workflow:


I don't think more coordination is involved - you just have multiple files in vignettes/. And, as you mentioned, it's a bonus that when a user downloads the annotation package they get all related workflows.

A fresh R session is started for each package but not for each vignette in the package.

Any thoughts would be appreciated. I'm also happy to be a guinea pig for
any SVN->Git transition for the workflow packages, if that's on the radar.

Nitesh has created git repos for the workflow packages and Andrzej is adapting the BBS code to incorporate them into the builds. We guesstimate this will be done by the end of the year. You shouldn't have to do anything on your end - once we're ready to switch over we'll let you know and send the new location of the workflow in git.



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