[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Robert M. Flight]

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
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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>
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 (which still works, but is probably outdated)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=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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