[Bioperl-l] Bio-perl and webpages?

Jérémy JUST jeremy_just at netcourrier.com
Tue Jul 19 11:25:32 EDT 2005

On Tue, 19 Jul 2005 15:31:05 +0100
Paulo Almeida <palmeida at igc.gulbenkian.pt> wrote:

> Insecure $ENV{PATH} while running with -T switch at 
> /usr/local/share/perl/5.8.4/Bio/Tools/Run/Alignment/Clustalw.pm line 
> 556, <GEN0> line 2.
> I wouldn't mind hardcoding the path of Clustal, but I couldn't figure 
> out a way to do it, or to untaint the variable. Can anyone help?

  The content of %ENV is considered as unsafe, since it comes from
outside your program.
  One secure way of untainting the PATH is to set it at the beginning of
your code:

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

  I think you are bound to hardcode the PATH into your program for it to
be really safe.
  I've seen another solution in the SpamAssassin code: it checks each
element of the PATH to verify that there is no world-writable or
group-writable directories in it.

  See also perldoc perlsec for more details.

Jérémy JUST  <jeremy_just at netcourrier.com>

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