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

Martin Morgan martin.morgan at roswellpark.org
Mon Nov 20 14:50:56 CET 2017

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 (which still works, but is probably outdated)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.


> 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
>>> -> 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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