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

The split-up workflows seem to have built successfully:

http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/

Is there something I have to do to get a blurb specific to each
vignette, as observed for "Annotation_Resources" vs
"Annotating_Genomic_Ranges"?

The various vignettes are ordered pedagogically, so the order in which
they are presented in the workflow page might require some manual
specification. It would also be nice if the multiple simpleSingleCell
workflows are grouped together, to avoid being intermingled with other
workflows on the page.

Finally, could we get a separate "single-cell workflows" section? The
current "Basic/Advanced" partition is pretty crude, and I can see
opportunities for more detailed stratification, e.g., by ChIP-seq,
RNA-seq, single-cell RNA-seq, proteomics (including mass cytometry).

Cheers,

Aaron


On 11/12/17 20:24, Aaron Lun wrote:

Thanks Val:

Obenchain, Valerie wrote:

Hi,

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

Following up on our earlier discussion:

https://stat.ethz.ch/pipermail/bioc-devel/2017-October/011949.html

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:

https://bioconductor.org/help/workflows/

I didn't know that, thanks.

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.

Ah. That's a shame, I was hoping to reduce the sensitivity to the DLL

limit.

But now that I think about it: maybe that's not actually a problem,
provided the BioC workflow builders have a high DLL limit. The main
issue was that *users* were running into the DLL limit; by splitting the
workflow up, users should no be tempted to run everything at once, thus
avoiding the limit on their machines. Of course, Bioconductor can
control its own build machines, so as long as they set the MAX_DLLs
high, it should still build and show up on the website.

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.

Cool, looking forward to it.

-A

Val

Cheers,

Aaron

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Aaron Lun
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University of Cambridge