Right, in all this, I was forgetting the vast amount of confusion with the Bioc GitHub mirror. I apologise.
Looking forward to having the web interface available. Robert On Mon, Nov 20, 2017, 17:08 Martin Morgan <martin.mor...@roswellpark.org> wrote: > On 11/20/2017 04:58 PM, Robert M. Flight wrote: > > So, what if there was a MetaBioconductor site and repo similar to the > > MetaCRAN project? https://www.r-pkg.org/about > > > > Not sure exactly who maintains it (probably someone at RStudio), but it > > is largely automatic I believe, and it provides a full GitHub archive of > > *all* the packages on CRAN, which if this were done for Bioconductor > > would satisfy what I think Steffen is looking for, as well as lots of > > other advantages. > > > > It also has the advantage that it looks like 90% of the work would be > > done for Bioconductor with likely very little work required for the > > Bioconductor Admins (ideally 100% of work would be done for them). > > there has been some discussion of that, e.g., > > https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html > > but we will not do it (maintain a github mirror), for instance because > some experiment data packages have commits that would require lfs, > because of issues with reliably syncing data, and because of confusion > it introduces on the 'official' repository. > > We do intend to provide a browsable interface to the official > git.bioconductor.org that would allow Steffen's use case during the > present release cycle; it is not currently available. > > A different solution would be to update the relevant ExperimentData > package to use ExperimentHub (see, e.g., > https://github.com/LTLA/TENxBrainData for a relatively simple example, > though not yet in Bioconductor) and the resource would then be available > at a URL https://annotationhub.bioconductor.org/fetch/... > > Martin > > > > > Just a thought. > > > > -Robert > > > > Robert M Flight, PhD > > Bioinformatics Research Associate > > Puller of Rabbits from Hats > > Research Parasite > > Resource Center for Stable Isotope Resolved Metabolomics > > Manager, Systems Biology and Omics Integration Journal Club > > Markey Cancer Center > > CC434 Roach Building > > University of Kentucky > > Lexington, KY > > > > Twitter: @rmflight > > Web: rmflight.github.io <http://rmflight.github.io> > > ORCID: http://orcid.org/0000-0001-8141-7788 > > EM rfligh...@gmail.com <mailto:rfligh...@gmail.com> > > PH 502-509-1827 <tel:(502)%20509-1827> > > > > To call in the statistician after the experiment is done may be no more > > than asking him to perform a post-mortem examination: he may be able to > > say what the experiment died of. - Ronald Fisher > > > > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan > > <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> > > wrote: > > > > On 11/19/2017 06:11 PM, Neumann, Steffen wrote: > > > Hi, > > > > > > thanks for the answer, unfortunately > > > not exactly what I meant. To be more precise: > > > > > > I want to point Galaxy to download (test) MS data files > > > from either the faahKO package, or msdata or mtbls2 in BioC. > > > > > > For that I need an ftp/http/https link to the files, > > > and I was able to use > > > > > > > > > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF > > > > > > (which still works, but is probably outdated) > > > So is there anything equivalent in the new git setup ? > > > > no, not from git.bioconductor.org <http://git.bioconductor.org>. > > > > Martin > > > > > > > > Yours, > > > Steffen > > > > > > > > > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote: > > >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote: > > >>> Hi, > > >>> > > >>> I would like to have a URL to individual files > > >>> we have in BioC packages. This is useful > > >>> e.g. if I need test data from, say, the msdata package, > > >>> in another context. > > >>> > > >>> In the SVN days, I was able to point directly > > >>> into the SVN repo with readonly:readonly access. > > >>> We also had the (now deprecated) way to link to: > > >>> > https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D > > >>> ESCRIPTION > > >>> > > >>> -> Is there anything comparable today ? > > >> > > >> I think the git archive command might do the trick, but it > requires > > >> ssh > > >> (i.e., write) access to the repository > > >> > > >> git archive --remote=g...@git.bioconductor.org:packages/xcms \ > > >> master DESCRIPTION | tar -xf - > > >> > > >> > > >>> > > >>> It could be as simple as a directory tree > > >>> of a working copies of all https://git.bioconductor.org/ > > >>> served by the apache (or whatever) web server, > > >>> or (a bit cooler) a gitweb or similar http interface. > > >>> > > >>> Wouldn't that be a fantastic christmas present > > >>> for us users and developers :-) ? > > >>> > > >>> Yours, > > >>> Steffen > > >>> > > >> > > >> > > >> 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. > > > > > > This email message may contain legally privileged > and/or...{{dropped:2}} > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto: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. 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