dimitris852 has asked for the wisdom of the Perl Monks concerning the following question:

Hello everyone.I m trying to run the script below. but I get the error:

------------- EXCEPTION ------------- MSG: Cannot find executable for clustalw. path="clustalw.exe" STACK Bio::Tools::Run::WrapperBase::executable C:/Perl64/site/lib/Bio/Tools/Run/ WrapperBase.pm:340 STACK Bio::Tools::Run::Alignment::Clustalw::_run C:/Perl64/site/lib/Bio/Tools/Ru n/Alignment/Clustalw.pm:752 STACK Bio::Tools::Run::Alignment::Clustalw::align C:/Perl64/site/lib/Bio/Tools/R un/Alignment/Clustalw.pm:515 STACK toplevel a.pl:29 

    #!/usr/bin/perl
    $ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2';
    use warnings;
    use strict;
    
    use Bio::AlignIO;
    use Bio::SeqIO;
    use Bio::Tools::Run::Alignment::Clustalw;
    
    my $file = <>; # Get file name from command prompt.
    my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix =>
+ 'BLOSUM');
    my $ktuple = 3;
    $factory->ktuple($ktuple);
    
    my $inseq = Bio::SeqIO->new(
                        -file => "<$file",
                        -format => "fasta"
                       );
    
    my $seq;
    my @seq_array;
    while ($seq = $inseq->next_seq) {
        push(@seq_array, $seq);
    }
    
    # Now we do the actual alignment.
    my $seq_array_ref = \@seq_array;
    my $aln = $factory->align($seq_array_ref);

[download]

How to make perl find my clustalw.exe???? I think that already did that by setting at the beginning the environmental variable $ENV{CLUSTALDIR}. Any help will be much appreciated!!!!

Replies are listed 'Best First'.
Re: Can't run Clustalw through Bioperl
by 1nickt (Canon) on Mar 14, 2016 at 01:58 UTC

    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;

...

    [download]

    Hope this helps!


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

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