[Bioperl-l] Bio::Tools::Run::Bowtie andBio::Assembly::IO::bowtie now available BETA

Chris Fields cjfields at illinois.edu
Mon Feb 22 13:46:39 EST 2010

On Mon, 2010-02-22 at 12:53 -0500, Mark A. Jensen wrote:
> ... I'm secretly working on is a package called WrapperMaker, that uses XML
> based on an XML Schema to define program names, commands, inputs and other 
> details
> (rather than an ugly Config module exporting hard to remember global variables),
> passing them to CommandExts and providing a nice WrapperBase object
> transparently. This is getting there, but isn't ready for primetime.)
> cheers MAJ

Sounds promising; I could foresee having a config-file based approach
usable across other Bio* languages; they would just need to come up with
similar wrappers and parsers.  Might be something to bring up with the
biopython/bioruby crowd.

Also, have you thought about possibly abstracting out parts so that one
could describe the relevant bits in alternative formats (JSON, YAML,
etc) other than XML?  Something like this might be handy:



More information about the Bioperl-l mailing list