[Bioc-devel] experimental data packages and git-lfs

[Turaga, Nitesh]

Hi Levi,

I’m not sure what you mean by tracked vs checked.

On another note, I have explored your package a little on GitHub (waldronLab/curatedOvarianData), and I’ve noticed that the data files there are stored as LFS files. As long as you don’t add the .gitattributes file in upstream, you should be fine. You can keep the LFS tracking on Github and non-LFS storage on bioc-git separate. 

To summarize:  No LFS support as of right now on bioc-git server, so I wouldn’t use any LFS commands.

Best,

Nitesh


> On Sep 6, 2017, at 3:05 PM, Levi Waldron <lwaldron.research at gmail.com> wrote:
> 
> Thank you, Nitesh.  Is there any difference at all now in how experimental data vs. software packages are tracked and checked?
> 
> On Tue, Sep 5, 2017 at 8:40 PM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
> Hi Levi,
> 
> The external_data_store.txt file is not needed anymore.
> 
> The current git.bioconductor.org server does not store files in the LFS mode, so you can just add a file, commit and push. But for Github, you might have to use LFS for such large files. I’ll look into this more and get back to you with a detailed reply.
> 
> Best,
> 
> Nitesh
> 
> > On Sep 5, 2017, at 4:49 PM, Levi Waldron <lwaldron.research at gmail.com> wrote:
> >
> > Also, can I now remove external_data_store.txt?
> >
> > $ cat external_data_store.txt
> > data
> > inst/extdata
> >
> >
> > On Tue, Sep 5, 2017 at 4:38 PM, Levi Waldron <lwaldron.research at gmail.com>
> > wrote:
> >
> >> Are a couple extra commands needed at https://www.bioconductor.
> >> org/developers/how-to/git/maintain-github-bioc/ for experimental data
> >> packages? I followed the instructions here for curatedOvarianData, but got
> >> GitHub warnings on push:
> >>
> >> remote: warning: GH001: Large files detected. You may want to try Git
> >> Large File Storage - https://git-lfs.github.com.
> >> remote: warning: See http://git.io/iEPt8g for more information.
> >> remote: warning: File data/TCGA_eset.rda is 53.10 MB; this is larger than
> >> GitHub's recommended maximum file size of 50.00 MB
> >>
> >> So I followed the instructions at https://git-lfs.github.com/:
> >>
> >> git lfs track "*.rda"
> >> git add .gitattributes
> >> git commit -a
> >>
> >> Does this seem correct, and is there anything else to know for
> >> experimental data packages with large files?
> >>
> >> --
> >> Levi Waldron
> >> http://www.waldronlab.org
> >> Assistant Professor of Biostatistics     CUNY School of Public Health
> >> US: +1 646-364-9616 <+1%20646-364-9616>
> >>         Skype: levi.waldron
> >>
> >
> >
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics     CUNY School of Public Health
> > US: +1 646-364-9616                                           Skype:
> > levi.waldron
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
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> 
> 
> -- 
> Levi Waldron                                              http://www.waldronlab.org
> Assistant Professor of Biostatistics     CUNY School of Public Health
> US: +1 646-364-9616                                           Skype: levi.waldron



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