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

Mark A. Jensen maj at fortinbras.us
Mon Apr 19 09:46:39 EDT 2010


great Chris-- yes, would be a good disc topic. thanks MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>; "Ben Bimber" <bimber at wisc.edu>
Sent: Monday, April 19, 2010 9:28 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::WrapperBase: Capture the commandthatis 
executed?


> 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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