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

Mark A. Jensen maj at fortinbras.us
Mon Apr 19 09:03:49 EDT 2010

Hey Ben,
Yes, the new stuff is in the bioperl-dev/trunk
(code.open-bio.org was working as of this morning...)

This is all pretty experimental, so use at own risk. The XML-based
config system is experimental too at the moment (tho' all code
is available, in bioperl-dev/trunk/Bio/Tools). I've been getting
good feedback from other Bio* peeps, who are advocating using an
existing config standard like emboss ACD or the Galaxy format.
I'll likely convert the wrappermaker system to using one of those,
but the custom format (in maker.xsd in bioperl-dev) will be there to
experiment with.

(To the list, any comments regarding this issue are welcome, see
 http://bioperl.org/wiki/HOWTO:Wrappers for an overview of
this project)

cheers MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Sent: Monday, April 19, 2010 8:27 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the command 
thatis executed?

ok, that's what i thought.  whenever i need to debug something i've
been hacking CommandExts to print @ipc_args, but that's kind of an
ugly solution.

related to this - now that XML is supported instead of text-based
config files, is there a subversion repository where anyone is
gathering these files?  i saw your web-based XML generator, which is


On Mon, Apr 19, 2010 at 7:05 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
> 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 executed?
>> 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.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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