[Bioc-devel] Experiment data packages
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 https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/<PKG> Changes to the package itself (e.g., version bump, documentation) need to be commited to https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/<PKG> 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 data_store/chromstaRData/data/experiment_table.RData 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 https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/add_data.py svn co https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/chromstaRData ./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]]
_______________________________________________ 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...{{dropped:2}}