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

Aaron Lun alun at wehi.edu.au
Sun Apr 1 20:17:09 CEST 2018

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, Hervé Pagès 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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