On 06/05/2013 03:33 PM, Peter Cock wrote:
On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chilton@msi.umn.edu wrote:
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- Finally, an idea - "Death to RPY - The BoF". Everyone with a stake
in this meets with laptops at the Galaxy conference together and we divvy up the remaining tools to convert (hopefully one tool per person). Every person is also assigned two of the existing converted tools to retest and clean up. As they are completed they are given to a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to collect, re-retest, and okay. The changes are then committed all together at the end and the next Galaxy release contains no dependencies on rpy.
These tools are not updated frequently, so the advantage of these all being upgraded in one commit before being shipped off to the tool shed is that an institution that is really stuck on rpy1 for whatever reason can just undo that single commit and keep going with the old tools indefinitely.
If anybody with commit access signs on I will be happy create a BoF page and attend this.
Thanks, -John
If you all can pull that off in Oslo, great. Otherwise a piecewise conversion seems a sensible plan B, where both rpy (v1) and rpy2 are installed and things are updated on a tool by tool basis.
The BoF group might also have some collective wisdom on how to deal with the question of multiple versions of R/BioConductor given this is important for reproducibility of many more complex and rapidly developed R tools.
Peter
I like the BoF suggestion, I am just afraid we will be too busy in Oslo to do it...we probably have to go for Peter's back-up plan. And, thank to JJ's efforts we are already well into the piecewise conversion.
As part of our current work to set up a new box for our Galaxy development server at the FMI, we will use the already converted tools. I'll keep you posted.
Regarding "the question of multiple versions of R/BioConductor": we intend to keep them, and if necessary 'freeze' a tool...but we are looking for a better solution.
Regards, Hans-Rudolf