[Bioc-devel] Git lfs support

[Anatoly Sorokin]

Hi Hervé,

I've made a new package with metadata.csv, as described in
CreateAnAnnotationPackage
vignette.

The data is located on the public service as a zipped SQLite database. So
I've set both SourceType and DispatchClass as 'Zip'.
From AnnotationHub::DispatchClassList() I expect that I should have an
unzipped file path. My first question is: how do I get that path?

The second question is: what should I put into make-data.R? The database is
already created, cleaned and validated. All I need for the package is to
download it, unzip and connect.

Thank you,
Anatoly

On Thu, Aug 26, 2021 at 12:59 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> 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
>

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