[Bioperl-l] Bioperl-run Wrappers

[Chris Fields]

On Jan 28, 2011, at 12:18 PM, Ben Bimber wrote:

> Hello,
> 
> I'm using CommandExts to wrap a number of tools.  In a pipeline I was
> looking to make the tools log their current version.  I realized that
> instead of using run() in a unique way for each tool, perhaps there
> should be a consistent method that gets called and returns a version
> string.  because obtaining this version string is specific to the
> tool, perhaps each wrapper could provide a version() method that runs
> the appropriate command on the executable, parses, then returns some
> string.  has something like this been discussed?  have others already
> solved this?
> 
> Thanks,
> Ben

(apologies for the late response, maybe you worked it out?)

If you mean a version string for the wrapped tool, there is a Bio::Tools::Run::WrapperBase method called version() I believe (not implemented for obvious reasons, but implemented by each wrapper as needed).  If you want a specific version of the module (say, an API version) you may want to assign $VERSION or create a new global ($API_VERSION, perhaps) in case it conflicts with the BioPerl core version.

chris