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GMOD/Admin/Update/WormBase.pm  view on Meta::CPAN

  unless ($adaptor->dl_only) {
    $self->logit(-msg => "Unpacking and installing $acedb");
    chdir($acedb_path);
    system("gunzip -c $local_path/$acedb | tar -x --no-same-owner -f -");
    unlink($acedb_path . '/elegans');
    symlink("elegans_$version",'elegans');

    # Adjust permissions
    my $command = <<END;
chown -R acedb $acedb_path/elegans*
chgrp -R acedb $acedb_path/elegans*
chmod 2775 $acedb_path/elegans*
##chown acedb $acedb_path/bin/*
##chgrp acedb $acedb_path/bin/*
END

    $self->test_for_error(system($command),"Fetching and installing acedb for WormBase");
  }
}


sub fetch_elegans_gff {
  my ($self,@p) = @_;

GMOD/Admin/Update/WormBase.pm  view on Meta::CPAN

    $self->logit(-msg => "Unpacking and installing $gff");
    my $command = <<END;
cd $mysql_path
mv elegans elegans.bak
mv elegans_pmap elegans_pmap.bak
gunzip -c $local_path/$gff | tar xvf -
rm -rf elegans.bak
rm -rf elegans_pmap.bak
chgrp -R mysql elegans_pmap
chgrp -R mysql elegans
chown -R mysql elegans_pmap
chown -R mysql elegans
END

    $self->test_for_error(system($command),"Fetching and installing C. elegans GFF database for WormBase");
  }
}

sub fetch_blast_blat {
  my ($self,@p) = @_;
  $self->logit(-msg=>'Fetching and installing BLAST databases',
	       -emphasis => 1);

GMOD/Admin/Update/WormBase.pm  view on Meta::CPAN

  my $mysql_path = $adaptor->mysql_path;
  unless ($adaptor->dl_only) {
    $self->logit(-msg => "Unpacking and installing $gff");
    my $command = <<END;
cd $mysql_path
mv briggsae briggsae.bak
gunzip -c $local_path/$gff | tar -xf -
rm -rf briggsae.bak
chgrp -R mysql briggsae
chown -R mysql briggsae
END

    $self->test_for_error(system($command),"Fetching and installing C. briggsae GFF database for WormBase");
  }
}


# THe libraires are not included above
# This really needs to be worked in
# This will only be used for WormBase packages