On 06/05/2013 03:33 PM, Peter Cock wrote:
On Wed, Jun 5, 2013 at 2:18 PM, John Chilton <chil...@msi.umn.edu> wrote:


- 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.


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.


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

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