[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?
Robert M. Flight
rflight79 at gmail.com
Mon Nov 20 23:15:22 CET 2017
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.morgan at 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 rflight79 at gmail.com <mailto:rflight79 at 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.morgan at roswellpark.org <mailto:martin.morgan at 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=git at 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
> > >>>
> > >>
> > >>
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