The other thing Steffen could do is keep personal clones of those packages on GitHub, but that's probably not ideal.
-Robert On Mon, Nov 20, 2017 at 4:58 PM Robert M. Flight <rfligh...@gmail.com> 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). > > 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 > ORCID: http://orcid.org/0000-0001-8141-7788 > EM rfligh...@gmail.com > PH 502-509-1827 <(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> 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 (which still works, but is probably outdated) 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. >> >> 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 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
