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. -A 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-boun...@r-project.org> on behalf of > Aaron Lun <a...@wehi.edu.au> > Sent: Sunday, April 1, 2018 2:17:09 PM > To: Hervé Pagès; bioc-devel@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. > > > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is prohibited. If > you have received this message in error, please notify the sender > immediately by e-mail and delete this email message from your > computer. 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