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

Hervé Pagès hpages at fredhutch.org
Fri Sep 8 01:25:16 CEST 2017

Hi Levi,

On 09/07/2017 02:52 PM, Levi Waldron wrote:
> Thanks, Nitesh! See below:
> On Thu, Sep 7, 2017 at 4:21 PM, Turaga, Nitesh <
> Nitesh.Turaga at roswellpark.org> wrote:
>> Hi Levi,
>> I’m not sure what you mean by tracked vs checked.
> Sorry, I meant whether there are any differences in the way software and
> experimental data packages are handled by Bioconductor. It seems like from
> the developer's perspective now, they are handled exactly the same, as
> opposed to in the past when experimental data packages were tracked in two
> separate svn repos and checked only twice a week.

I'll try to summarize what has changed with respect to software vs
data-experiment packages:

What has changed with the old svn way is that software and
data-experiment packages are now in the same location on the new
git.bioconductor.org server. Also now developers access and maintain
both types of packages the same way thru the git client. No more
separation between package shell and data for data-experiment packages.
So the external_data_store.txt file is no more needed.

What has NOT changed is that builds for software and data-experiment
packages are still separated. Both still happen every day but at
different times and we still generate separate reports. Also for
the last couple of years or so, we've been building/checking
data-experiment packages on Linux only. This is for lack of resource.
Software and data-experiment packages are still propagated to
separate public repositories:

   in release:

   in devel

You can see this by calling biocinstallRepos() after loading the
BiocInstaller package.
Finally our requirements for software and data-experiment packages
have not changed either. The latter can be bigger than the former and
they are not required to have a vignette. Also they should NOT have
native code in them.


> 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.
> So the way I understand this is, I can continue using LFS on GitHub, and
> merging my changes upstream to git.bioconductor.org, as long as I avoid
> adding the .gitattributes file upstream. I have already used LFS commands
> to initiate LFS on GitHub, but these shouldn't affect git.bioconductor.org
> if I avoid adding the .gitattributes file upstream.
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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