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

Hervé Pagès hpages at fredhutch.org
Fri Mar 30 22:10:28 CEST 2018

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

The canonical location for the workflow source code now is

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:


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:


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

Let us know if you have any question about this.


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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