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

Wolfgang Huber wolfgang.huber at embl.de
Sat Mar 31 20:36:55 CEST 2018

Thank you, Lori, Valerie, Andrzej, Nitesh and  Hervé, this is great 
news! This should help further rationalize the authoring and maintenance 
of workflows.

I'm sure many have also seen the call to submit workflows to the 
Bioconductor gateway on F1000Research 
https://support.bioconductor.org/p/107477/ - which will make your 
workflow a 'peer-reviewed' publication and gives it additional visibility.

  Best wishes

30.3.18 22:10, Hervé Pagès scripsit:
> 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.

With thanks in advance-

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de

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