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

Aaron Lun alun at wehi.edu.au
Tue Apr 3 13:49:59 CEST 2018

It would also be nice to have a mechanism to obtain the underlying *.md
files used to generate the compiled workflow HTMLs. I've been using
this to check that the results have not changed since the last run.

Of course, I could also do this locally, but it would be reassuring to
confirm that the workflow is building correctly on the BioC machines.


On Mon, 2018-04-02 at 11:42 +0000, Shepherd, Lori wrote:
> For now the page at 
> https://www.bioconductor.org/help/workflows/
> 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. 
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
> 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: Hervé Pagès; 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:
> https://www.bioconductor.org/help/workflows/
> ... be updated to reflect changes in the git repositories for the
> workflows? 
> 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.
> Cheers,
> Aaron
> 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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