in reply to Can't run Clustalw through Bioperl

The documentation for Bio::Tools::Run::Alignment::Clustalw says that the environment variable needs to be set in a BEGIN block, so that the module can find the executable. Did you try that? 

BEGIN { $ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2'; }
use warnings;
use strict;
    
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Tools::Run::Alignment::Clustalw;

...

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Hope this helps!


The way forward always starts with a minimal test.

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Re^2: Can't run Clustalw through Bioperl
by dimitris852 (Acolyte) on Mar 14, 2016 at 02:07 UTC
    I ve tried it so far. Same error again!
[reply]

      Are you sure the program is installed in the path you are specifying, and it's executable? What is the output of: 

      C:\> where clustalw.exe

      [download]
      ? What happens if you try to run it by hand in its folder?

      ( Disclaimer: I don't use MS Windows, but I believe that's the command... )


      The way forward always starts with a minimal test.
[reply]
[d/l]

        --->INFO: Could not find files for the given pattern(s).

        But i can see it. Its already installed on my computer and the Clusterw.exe is on this specific path. really confused...

[reply]

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