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  • BioPerl installation and execution problem

    I have installed activeperl in windows xp.
    through Perl Package Manager i have installed BioPerl repositories.
    but while trying to execute BioPerl program..
    #!/usr/bin/env perl
    use Bio::Seq;
    use Bio::SeqIO;

    # create a sequence object of some DNA
    my $seq = Bio::Seq->new(-id => 'testseq', -seq => 'CATGTAGATAG');

    # print out some details about it
    print "seq is ", $seq->length, " bases long\n";
    print "revcom seq is ", $seq->revcom->seq, "\n";

    # write it to a file in Fasta format
    my $out = Bio::SeqIO->new(-file => '>testseq.fsa', -format => 'Fasta');
    $out->write_seq($seq);

    the following error is coming

    Cant locate Bio/Seq.pm in @INC <INC contains : C:/Perl/site/lib C:/Perl/lib.> at C:\Perl\bin\Sequence.pl line1.
    BEGIN failed--compilation aborted at C:\Perl\bin\Sequence.pl line1.

    what is the problem here??

    How to identify whether BioPerl is installed or not???

    Please guide me....

    thanks & Regards

  • #2
    That error you see "Can't locate Bio/Seq.pm ..." means that Perl cannot find BioPerl in the standard places that libraries are installed (referred to as PERL5LIB or @INC). You might want to review the install process to ensure that it was successful and try to find out if it was installed somewhere other than what is listed in that error message. If you are using a package manager then it will probably install in a standard location, so the installation likely did not succeed. I should warn that I have no experience with Windows and PPM, but what you are seeing is a standard complaint from Perl. If you can't find a solution, you could try sending your message to the BioPerl listserv, as there are sure to be people there with experience installing on Windows.

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