[Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the command thatis executed?

Mark A. Jensen maj at fortinbras.us
Mon Apr 19 08:05:42 EDT 2010

For the entire command line (program + parameters), there isn't a single place 
in WrapperBase where that is collected. WrapperBase::_setparams() produces the 
option string that can then  be appended to the program name for subsequent 
execution. In WrapperBase::CommandExts::_run(), the command line options are 
generated with _setparams, then passed to IPC::Run for a generic execution 
scheme. It would be easy enough from CommandExts to record the full command in a 
suitable object property; it's a good idea.
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Sunday, April 18, 2010 4:30 PM
Subject: [Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the command thatis 

> If I write a wrapper for a program using Bio::Tools::Run::WrapperBase,
> is there an easy way to capture a string of the exact command that was
> executed?  This would sometimes be useful for debugging / logging.
> There are functions to capture stdout/stderror, but i did not see
> anything with the command itself.  i could well have missed it though.
> Thanks.
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> Bioperl-l at lists.open-bio.org
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