[Bioperl-l] IPC/Run.pm?

Chris Fields cjfields at illinois.edu
Wed Oct 20 21:54:48 EDT 2010


+1.  Quite a few modules there use it.

chris

On Oct 20, 2010, at 8:21 PM, Mark A. Jensen wrote:

> I would +1 making IPC::Run required. It's got some nice features and it much safer than system(). Might even want to make it a dev recommendation for all system calls. MAJ
> 
>> -----Original Message-----
>> From: Robert Buels [mailto:rmb32 at cornell.edu]
>> Sent: Wednesday, October 20, 2010 08:27 PM
>> To: 'Chris Fields'
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] IPC/Run.pm?
>> 
>> Ah, the joys of optional deps.
>> 
>> You know, bioperl-run does not have that many deps right now.  Why don't 
>> we just make those optional ones required?
>> 
>> R
>> 
>> 
>> Chris Fields wrote:
>>> If you mean IPC::Run, I'm not sure.  I don't think BioPerl-Run was ever a part of Strawberry Perl Pro.
>>> 
>>> I do know there are some warnings that will pop up with BioPerl when using perl 5.12; these have been fixed in the github repo but haven't made their way into a release yet.
>>> 
>>> chris
>>> 
>>> On Oct 19, 2010, at 3:38 PM, T D wrote:
>>> 
>>>> Thank you. I downloaded IPC::Run and the code seems to be working now. Is
>>>> Run.pm no longer part of the latest Strawberry Perl installation (v5.12.1)?
>>>> 
>>>> 
>>>> On Tue, Oct 19, 2010 at 1:33 PM, Chris Fields <cjfields at illinois.edu> wrote:
>>>> 
>>>>> No, IPC::Run is different than IPC::Run3:
>>>>> 
>>>>> http://search.cpan.org/dist/IPC-Run/
>>>>> http://search.cpan.org/dist/IPC-Run3/
>>>>> 
>>>>> Both should work under Windows, not sure about Windows7 but I can't see why
>>>>> they wouldn't work.
>>>>> 
>>>>> chris
>>>>> 
>>>>> On Oct 19, 2010, at 12:28 PM, T D wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I'm new to BioPerl and Perl in general, and I'm trying to get
>>>>>> StandAloneBlastPlus to run. I got the latest versions using git and
>>>>>> downloaded bioperl-live  and bioperl-run.  I am having issues with Perl
>>>>> not
>>>>>> finding modules. Here is my error:
>>>>>> 
>>>>>> Can't locate IPC/Run.pm in @INC
>>>>>> 
>>>>>> Where is this module located? I am running Windows 7. I did a search for
>>>>> the
>>>>>> Run.pm and could only find IPC/*Run3.pm* under my Perl installation. Is
>>>>>> Run.pm the older version? I have Perl v5.12.1 installed.
>>>>>> 
>>>>>> Thanks in advance!
>>>>>> Tracey
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>>>>> 
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