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

[Levi Waldron]

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
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.




-- 
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]]