[Bioc-devel] Git lfs support

[Hervé Pagès]

Hi Anatoly,

Let's keep this conversation on the bioc-devel mailing list where it 
started.

On 26/08/2021 02:46, Anatoly Sorokin wrote:
> Hi Hervé,
> 
> thank you for your answer. Does this mean that the SQLite file will be 
> downloaded separately and kept in some cache?

Yes.

> 
> And another question: does this mean that there should be two packages, 
> one for code and another one for the database?

Yes. One is what we call the software package and the other one the 
accompanying data package.

Cheers,
H.

> 
> On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès <hpages.on.github using gmail.com 
> <mailto:hpages.on.github using gmail.com>> wrote:
> 
>     Hi Anatoly,
> 
>     What kind of data is in your SQLite database? The Bioconductor approach
>     for this is to provide the data as a separate data annotation or data
>     experiment package. More precisely, the data itself should go on
>     AnnotationHub or ExperimentHub. It should be associated with a "Hub
>     package", that is, a data package that documents it and explains how to
>     retrieve it from AnnotationHub or ExperimentHub. See vignettes in the
>     HubPub package for more information:
> 
>     http://bioconductor.org/packages/HubPub
>     <http://bioconductor.org/packages/HubPub>
> 
>     Best,
> 
>     H.
> 
>     On 24/08/2021 17:53, Nitesh Turaga wrote:
>      > Hi,
>      >
>      > We don’t have LFS support on the Bioconductor git server.
>      >
>      > I would suggest finding an alternative.
>      >
>      > Best,
>      >
>      >
>      >
>      >
>      > Nitesh Turaga
>      > Scientist II, Department of Data Science,
>      > Bioconductor Core Team Member
>      > Dana Farber Cancer Institute
>      >
>      >> On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin <lptolik using gmail.com
>     <mailto:lptolik using gmail.com>> wrote:
>      >>
>      >> Hi all,
>      >>
>      >> we have developed a package that provides access to the data in
>     the locally
>      >> stored SQLite database. The GitHub Action successfully built the
>     package,
>      >> but in Bioconductor, it got an error. The only reason for the
>     error is that
>      >> the database itself is stored on GitHub via git-lfs, and the R
>     code got an
>      >> lfs placeholder instead of the actual database.
>      >>
>      >> Is it possible to activate lfs within Bioconductor automatic
>     building
>      >> server? The database is tiny (80 Mb), but I don't want to have
>     it as a
>      >> regular git object.
>      >>
>      >> Thank you,
>      >> Anatoly
>      >>
>      >>      [[alternative HTML version deleted]]
>      >>
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>      >
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>      >
> 
>     -- 
>     Hervé Pagès
> 
>     Bioconductor Core Team
>     hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
> 

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com