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

[Chris Fields]

Mark,

I think coming up with a cross-Bio* standard for wrappers is a very good idea, and would be worth further discussion here on-list and maybe at BOSC.  Centralizing around Galaxy is a good idea, though we may need to look into embellishing it if it doesn't suit all our needs.

Re: ACD, we essentially have the code for parsing ACD already in bioperl-run (I think Bio::Tools::Run::EMBOSSacd).

chris

On Apr 19, 2010, at 8:03 AM, Mark A. Jensen wrote:

> Hey Ben,
> Yes, the new stuff is in the bioperl-dev/trunk
> svn://code.open-bio.org/bioperl/bioperl-dev/trunk/Bio/Tools/Run
> (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
> useful.
> 
> -ben
> 
> 
> 
> 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.
>> MAJ
>> ----- 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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