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 at gmail.com <mailto:rflight79 at 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 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
>
>
>
> (which still works, but is probably outdated)
> So is there anything equivalent in the new git setup ?
>
> 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:
>>>
>>> ESCRIPTION
>>>
>>> -> Is there anything comparable today ?
>>
>> I think the git archive command might do the trick, but it
>> 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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