[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer

Hilmar Lapp hlapp at gmx.net
Wed Feb 28 23:16:38 EST 2007

On Feb 28, 2007, at 5:54 PM, Mark Johnson wrote:

> I don't like using system() due to issues with
> signals (Such as the user hitting ctrl-c and taking out the  
> child).  I feel
> better knowing the wrapped executable is in another process  
> disconnected
> from the console.

I'm not sure how the user would be able to take out the child hitting  
ctrl-c if you run it through system() (except if the parent  
terminates first - but maybe then terminating a run-away child is in  
good order).

I haven't read the IPC::run POD in full detail but you will want to  
make sure that if the parent gets killed the child does get killed  
too, or otherwise you'll have a run-away process that novices will  
have trouble with understanding or terminating.

Other than that though IPC::run seems like a useful module, so  
incurring this as a dependency should be fine.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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