[Bioc-devel] experimental data packages and git-lfs
lwaldron.research at gmail.com
Wed Sep 6 21:05:20 CEST 2017
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.
> > On Sep 5, 2017, at 4:49 PM, Levi Waldron <lwaldron.research at gmail.com>
> > 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
> >> 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
> >> 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]]
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