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

[Robert M. Flight]

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 <rflight79 at 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
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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 (which still works, but is probably outdated)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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