[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?
Mike Smith
gr|mbough @end|ng |rom gm@||@com
Mon May 10 11:59:44 CEST 2021
Hi Steffen,
Thanks for the feedback. I've been referencing this email thread when
presenting about developing the code website, so it might be old but it
wasn't forgotten!
Right now I think we still don't quite meet your use case, as
https://code.bioconductor.org/ currently only lists the software packages,
so msdata can't actually be found there. That choice was because I had
limited disk-space in my prototypes of the site and so didn't try copying
any other type of package, but it doesn't have to remain that way. I don't
know how much space might be needed for the other types of package, and
it's something I'm happy to consider for the future.
Cheers,
Mike
On Mon, 10 May 2021 at 09:10, Neumann, Steffen <sneumann using ipb-halle.de>
wrote:
> Hi,
>
> this is a follow-up to a rather old thread, but with
> Mike Smith's (twitter: @grimbough)
>
> https://code.bioconductor.org/
>
> We now have exactly what I had been looking for.
> Thanks Mike and BioC team !
>
> Yours,
> Steffen
>
> On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan 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 using gmail.com <mailto:rflight79 using 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 using roswellpark.org <mailto:
> > > martin.morgan using 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 using 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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