[Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Mon Apr 2 13:42:05 CEST 2018

For now the page at


will remain and be updated accordingly however there is discussion about having this page be removed or redirected.

In the next few days I hope to have the new landing pages up and running and will make an announcement when they are live. The new changes involve having a link to the workflows on the biocViews page, that will directly link to a workflow package landing page (like the software, annotation, and experiment package do).

Until the release your changes will be visible in devel which will transition over to the new release just as done for software packages -

The workflow are built monday, wednesday, and friday and the new landing pages will reflect when the package is propagated like the other types of packages.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Aaron Lun <alun at wehi.edu.au>
Sent: Sunday, April 1, 2018 2:17:09 PM
To: Herv� Pag�s; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Thanks everybody, this is much appreciated.

On that note, will the compiled workflows shown at:


... be updated to reflect changes in the git repositories for the

Or will the workflow page just directly link to the landing page for
each package? This would be very convenient, not least because it will
avoid me having to make pull requests to the bioconductor.org
repository every time I want to change my workflow blurb.

I'm in the process of fixing and updating my various workflows, and I'm
wondering when/how my changes will be visible to users.



On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> To the authors/maintainers of the workflows:
> Following the svn-to-git migration of the software and data
> experiment
> packages last summer, we've completed the migration of the workflow
> packages.
> The canonical location for the workflow source code now is
> git.bioconductor.org
> Please use your git client to access/maintain your workflow the same
> way you would do it for a software or data-experiment package.
> We've also migrated the workflows to our in-house build system.
> Starting with Bioc 3.7, the build report for the devel versions of
> the workflows can be found here:
>    https://bioconductor.org/checkResults/devel/workflows-LATEST/
> We run these builds every other day (Mondays, Wednesdays, Fridays).
> Because of limited build resources, we now run the data-experiment
> builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
> The links to the package landing pages are not working yet. This
> will be addressed in the next few days.
> Please address any error you see on the report for the workflow
> you maintain.
> Note that, from now on, we're also following the same version scheme
> for these packages as for the software and data-experiment packages.
> That is, we're using an even y (in x.y.z) in release and an odd y in
> devel. We'll take care of bumping y at release time (like we do for
> software and data-experiment packages).
> After the next Bioconductor release (scheduled for May 1), we'll
> start
> building the release versions of the workflows in addition to the
> devel versions. The build report for the release versions will be
> here:
>    https://bioconductor.org/checkResults/release/workflows-LATEST/
> Finally, please note that with the latest version of BiocInstaller
> (1.29.5), workflow packages can be installed with biocLite(), like
> any other Bioconductor package. We'll deprecate the old mechanism
> (workflowInstall()) at some point in the future.
> Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> migration.
> Let us know if you have any question about this.
> H.

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