Thanks Andrzej. > Thank you. I've edited the workflow index page by introducing a separate > "Single-cell Workflows" section, and by substituting the previous link to > your workflow by links to the individual parts.
Great, I'm looking forward to seeing it. Do you know how frequently the index page (I assume we're talking about https://bioconductor.org/help/workflows/) updates? I assume your edits haven't propagated through the system yet. > As discussed during EuroBioc, I'm happy to restructure the index page by > grouping workflows by topic. It would be really helpful if authors would > chime in to suggest the most relevant sections for their workflows. I can chip in with two that I'm involved in: "Differential Binding from ChIP-seq data <https://bioconductor.org/help/workflows/chipseqDB/>" => ChIP-seq workflows "Gene-level RNA-seq differential expression and pathway analysis <https://bioconductor.org/help/workflows/RnaSeqGeneEdgeRQL/>" => RNA-seq workflows Of course, it depends on how granular you want the topics to be. For example, I only see one ChIP-seq workflow, so that particular section might be a bit lonely for a while (I am planning to split that into two workflows later). Cheers, Aaron > On Tue, Dec 12, 2017 at 7:19 PM, Aaron Lun <aaron....@cruk.cam.ac.uk> wrote: > >> The split-up workflows seem to have built successfully: >> >> http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/ >> >> Is there something I have to do to get a blurb specific to each >> vignette, as observed for "Annotation_Resources" vs >> "Annotating_Genomic_Ranges"? >> >> The various vignettes are ordered pedagogically, so the order in which >> they are presented in the workflow page might require some manual >> specification. It would also be nice if the multiple simpleSingleCell >> workflows are grouped together, to avoid being intermingled with other >> workflows on the page. >> >> Finally, could we get a separate "single-cell workflows" section? The >> current "Basic/Advanced" partition is pretty crude, and I can see >> opportunities for more detailed stratification, e.g., by ChIP-seq, >> RNA-seq, single-cell RNA-seq, proteomics (including mass cytometry). >> >> Cheers, >> >> Aaron >> >> >> On 11/12/17 20:24, Aaron Lun wrote: >>> Thanks Val: >>> >>> Obenchain, Valerie wrote: >>>> Hi, >>>> >>>> On 12/11/2017 08:49 AM, Aaron Lun wrote: >>>>> Following up on our earlier discussion: >>>>> >>>>> https://stat.ethz.ch/pipermail/bioc-devel/2017-October/011949.html >>>>> >>>>> I have split the simpleSingleCell workflow into three (four, if you >>>>> include the introductory overview) self-contained Rmarkdown files. I am >>>>> preparing them for submission to BioC's workflow builder, and I would >>>>> like to check what is the best way to do this: >>>>> >>>>> i) Each workflow file goes into its own package. >>>>> >>>>> ii) All workflow files go into a single package. >>>>> >>>>> Option (i) is logistically easier but probably a bit odd conceptually, >>>>> especially if users need to download "simpleSingleCell1", >>>>> "simpleSingleCell2", "simpleSingleCell3", etc. >>>>> Option (ii) is nicer but requires more coordination, as the BioC >> webpage >>>>> builder needs to know that that multiple HTMLs have been generated. >> It's >>>>> also unclear to me whether this will run into problems with the DLL >>>>> limit - does R restart when compiling each vignette? >>>> You could do either but I'd say option 2 is easier from a maintenance >>>> standpoint and probably for the user. Maybe you've seen this but an >>>> example is the annotation workflow package which houses 2 workflows: >>>> >>>> ~/repos/svn/workflows >ls annotation/vignettes/ >>>> Annotating_Genomic_Ranges.Rmd Annotation_Resources.Rmd >>>> databaseTypes.png display.png >>>> >>>> Each has an informative name and is presented on the website as an >>>> individual workflow: >>>> >>>> https://bioconductor.org/help/workflows/ >>> I didn't know that, thanks. >>> >>>> I don't think more coordination is involved - you just have multiple >>>> files in vignettes/. And, as you mentioned, it's a bonus that when a >>>> user downloads the annotation package they get all related workflows. >>>> >>>> A fresh R session is started for each package but not for each >>>> vignette in the package. >>> Ah. That's a shame, I was hoping to reduce the sensitivity to the DLL >> limit. >>> But now that I think about it: maybe that's not actually a problem, >>> provided the BioC workflow builders have a high DLL limit. The main >>> issue was that *users* were running into the DLL limit; by splitting the >>> workflow up, users should no be tempted to run everything at once, thus >>> avoiding the limit on their machines. Of course, Bioconductor can >>> control its own build machines, so as long as they set the MAX_DLLs >>> high, it should still build and show up on the website. >>> >>>>> Any thoughts would be appreciated. I'm also happy to be a guinea pig >> for >>>>> any SVN->Git transition for the workflow packages, if that's on the >> radar. >>>> Nitesh has created git repos for the workflow packages and Andrzej is >>>> adapting the BBS code to incorporate them into the builds. We >>>> guesstimate this will be done by the end of the year. You shouldn't >>>> have to do anything on your end - once we're ready to switch over >>>> we'll let you know and send the new location of the workflow in git. >>> Cool, looking forward to it. >>> >>> -A >>> >>>> Val >>>>> Cheers, >>>>> >>>>> Aaron >>>>> _______________________________________________ >>>>> 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. Thank you. >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> -- >> Aaron Lun >> Research Associate, CRUK Cambridge Institute >> University of Cambridge >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel