[Bioperl-l] can't start 'water'

[Vesko Baev]

Hi,
In my computer I have bioperl-pack & Bioperl-run-pack, and I HAVE water.pm,but:
message in dos-prompt:

-------------------- WARNING ---------------------
MSG: Application [water] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at water.pl line 22.

Here is my script:
#!usr/bin/perl
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
  my $seqobj1 = Bio::Seq->new(-seq => "gacgggtatctttaggcggacttagg");
  my $seqobj2 = Bio::Seq->new(-seq => "gacgtgtatctttaggcggtcttacc");
  my @seqs_to_check; # this would be a list of seqs to compare   
  push (@seqs_to_check,seqobj2);
  # get an EMBOSS application object from the EMBOSS factory
  $factory = new Bio::Factory::EMBOSS;
#  $application = $factory->program('embossversion');
  # run the application with an optional hash containing parameters
#  $result = $application->run(); # returns a string or creates a file
#  print $result . "\n";

  $water = $factory->program('water');

  # here is an example of running the application
  # water can compare 1 seq against 1->many sequences
  # in a database using Smith-Waterman

  my $wateroutfile = 'mirna.water';
  $water->run({ '-sequencea' => $seqobj1,

              '-seqall'    => \@seqs_to_check,
              '-gapopen'   => '10.0',
              '-gapextend' => '0.5',
              '-outfile'   => $wateroutfile});
  # now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = new Bio::AlignIO(-format => 'emboss',
			       -file   => $wateroutfile);

  while( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

AND when I wrote 'use Bio::Tools::Run::PiseApplication::water;'
the message was:
Can't locate XML/Parser/PerlSAX.pm in @INC?!?!?!

WHAT TO DO?
Vesko
Thenks!!



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