[Bioperl-l] Stratopan as a strategy for reproducible code

Fields, Christopher J cjfields at illinois.edu
Fri Nov 15 03:29:15 UTC 2013

That’s a pretty nice service; we’ll definitely have a look into it.  Thanks for the pointer David!


On Nov 13, 2013, at 10:52 PM, David Mertens <dcmertens.perl at gmail.com> wrote:

> Hey all -
> I wanted to draw everyone's attention to Stratopan.com. It is a new
> website/cloud service run by Jeffrey Thalhammer, author of Perl::Critic. It
> is a publicly available instance of Pinto, which essentially lets you
> create your own mini-CPAN.
> This is a big deal for reproducibility. Stratopan lets you build a "stack"
> with a specific set of known-working modules. For example, this service
> lets you create a stack with the current version of BioPerl and any other
> modules that you use in your current research scripts. Stratopan will cache
> those versions and hold on to them FOREVER, or until you tell it to upgrade
> one or another module. Thus, if you created such a stack today, you could
> easily install that stack on a machine two years from now, and any scripts
> that you write now will work then.
> Obviously, you need to have a local::lib or similar setup so that you can
> install the modules from Stratopan, but that's not hard.
> For me, one of the major issues with my scientific code is that I
> frequently put developing modules to use before they're ready. A prime
> example of this is PDL::Graphics::Prima, my plotting library, which has
> (not surprisingly) undergone some backwards incompatible changes since I
> started working on it back in January, 2011. It's great to really test it
> out in live scientific code, but it sucks when I have to go back and clean
> up a large collection of scripts when I change the API. If I had Stratopan
> back in January 2011, I could have saved multiple versions of my plotting
> library, and kept my scripts working without the need to update them.
> Hope that helps!
> David
> -- 
> "Debugging is twice as hard as writing the code in the first place.
>  Therefore, if you write the code as cleverly as possible, you are,
>  by definition, not smart enough to debug it." -- Brian Kernighan
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