[Bioc-devel] Experiment data packages

Martin Morgan martin.morgan at roswellpark.org
Mon Jul 4 11:20:30 CEST 2016

On 07/04/2016 02:40 AM, Aaron Taudt wrote:
> Dear all,
> I am trying to update my experiment data package. I read the instructions
> at
> http://bioconductor.org/developers/how-to/source-control#experiment-data-packages
> but it's not clear to me at all how to do it the right way. The package
> infrastructure and data folders are stored in different repositories. When
> updating a package, do I make the changes in both repositories separately?
> What is the role of the python script to fold in the data? What does the
> external_data_store.txt file need to contain? The files that are stored in
> the "data_store" repository?

Changes to the large data need to be commited to


Changes to the package itself (e.g., version bump, documentation) need 
to be commited to


external_data_store.txt is a list of svn endpoints in the 
data_store/<PKG> that are to be folded into the checked-out pkgs/<PKG> 
hierarchy. Typically the end points in external_data_store.txt are 
folders, changes to the data replace files within folders that are 
already specified in external_data_store.txt, and there is no need to 
change external_data_store.txt.

 From SVN it looks like you want to change


and friends. It looks like external_data_store.txt already contained the 
path 'data', so that no change was necessary to this file. Having 
changed the content of the package, you would add a version bump to 
DESCRIPTION and commit pkgs/chromstaRData/DESCRIPTION. I think you've 
arrived at this state. I would have done something like

     svn co -N https://hedgehog.fhcrc.org/bioc-data/trunk/experiment
     cd experiment
     svn up pkgs/chromstaRData data_store/chromstaRData pkgs/add_data.py

make changes, and commit

     svn ci pkgs/chromstaRData data_store/chromstaRData

If things are successful, then in some temporary location checking out 
pkgs/chromstaRData and running the add_data.py script should result in a 
valid R package:

   cd /tmp
   svn export 
svn co 
./add_data.py chromstaRData

> It would be nice if there was a more detailed description on how to update
> experiment data packages. I'm not an expert in using svn and figuring this
> out by trial and error takes a lot of time because of the biweekly build
> cycles.
> Thanks,
> Aaron
> 	[[alternative HTML version deleted]]
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