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

[Neumann, Steffen]

Hi,

thanks everyone. In the short run I can certainly keep 
a personal copy, and in the long run Martin's solution 
will be exactly what I need, so no rush. 

Yours,
Steffen


On Mon, 2017-11-20 at 21:59 +0000, Robert M. Flight wrote:
> 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
> > 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 rflight79 at gmail.com
> > PH 502-509-1827
> > 
> > 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 roswel
> > lpark.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/msda
> > > ta/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/ma
> > > ster/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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