[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[K. Shameer]

Hello Jonny,

Are you sure that you have a compiled version of HMMER installed in your
machine ?

--
K. Shameer

> Hi,
>
> trying to run the example given for Bio::Tools::HMM on the Bioperl site,
> and
> when I try to run it, I get this in the command line...
>
> "The C-compiled engine for Hidden Markov Model (HMM) has not been
> installed.
>  Please read the install the bioperl-ext package
>
> BEGIN failed--compilation aborted at
> C:/strawberry/perl/site/lib/Bio/Tools/HMM.pm line 140.
> Compilation failed in require at HMM.txt line 4.
> BEGIN failed--compilation aborted at HMM.txt line 4."
>
> I have installed the entire bioperl-ext package through subversion, and it
> looks like all the relevant folders are in perl/site/lib/Bio/Tools, but it
> won't work.  Am I missing something?  I'm under the impression that the
> C-compiler comes with bioperl-ext (which installed with no reported
> problems)?  I concede that I am extrememly new to both Perl in general and
> Bioperl more specifically, but I have followed the instructions which I
> can
> find.  I have the bioperl core installed in addition to bioperl-db and
> bioperl-run.  I'm using Strawberry Perl on WinVista.  I appreciate that
> most
> work through Linux systems...I am at times sorely tempted myself.
>
> Any suggestions would be welcomed gratefully,
> cheers,
> Jonny
>
> ps.  this is the partial script I was trying to run...
>
> #!/usr/bin/perl -w
>
> usr strict;
> use Bio::Tools::HMM;
> use Bio::SeqIO;
> use Bio::Matrix::Scoring;
>
> #Create a HMM object
> #ACGT are the bases NC mean non-coding and coding
> $hmm = new Bio::Tools::HMM ('-symbols' => "ACGT", '-states' => "NC");
>
> #Initialise some training observation sequences
> $Seq1 = new Bio::SeqIO(-file => $ARGV[0], -format => 'fasta');
> $seq2 = new Bio::SeqIO(-file => $ARGV[1], -format => 'fasta');
> @seqs = ($seq1, $seq2);
>
> #Train the HMM with the observation sequences
> $hmm ->baum_welch_training(\@seqs);
>
> #Get parameters
> $init = $hmm->init_prob; #Returns an array reference
> $matrix1 = $hmm->transition_prob; #Returns Bio::Matrix::Scoring
> $matrix2 = $hmm->emission_prob; #Returns Bio::Matrix::Scoring
>
> I realise that this is incomplete.
> --
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>
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