[Bioperl-l] CGI taint solved

Chris Fields cjfields at uiuc.edu
Wed Feb 28 08:39:24 EST 2007

That could possibly clobber any other program calls from within the  
same script (unless they reside in /usr/local/bin) since you're  
explicitly assigning PATH, not appending:

$ENV{"PATH"} = '/usr/local/bin';

gets me (printing $ENV{"PATH"}):


whereas this:

$ENV{"PATH"} = '/usr/local/bin:' . $ENV{"PATH"};

gets me:


There's probably a File::* module that does this safely per OS flavor.


On Feb 28, 2007, at 4:50 AM, Neil Saunders wrote:

> Apologies for running a one-man thread, but I realised that I've  
> now answered my
> own question regarding errors with CGI, Bio::Factory::EMBOSS and  
> taint.
> Given that the EMBOSS binaries are in /usr/local/bin, adding:
> $ENV{'PATH'} = '/usr/local/bin'
> near the top of the script does the trick.
> Neil
> -- 
>   School of Molecular and Microbial Sciences
>   University of Queensland
>   Brisbane 4072 Australia
> http://nsaunders.wordpress.com
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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