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

[Martin Morgan]

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
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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 <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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