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lib/Bio/EnsEMBL/Analysis/Programs.pm  view on Meta::CPAN

    
    # For each program, check there is an executable
    foreach my $program (keys %Program_Paths) {
        
        # Deal with paths
        if ($program =~ m|/|) {
            _go_home( $H );
            my $path = $program;
            # Deal with tildes
            $path =~ s{^~([^/]*)}{ $1 ? (getpwnam($1))[7]
                                      : (getpwuid($>))[7] }e;
            if (my $real = _is_prog( $H, $path )) {
                $Program_Paths{ $program } = $real;
            }            
        }
        # Or search through all paths
        else {
            foreach my $path (@PATH) {
                _go_home( $H );
                if (my $real = _is_prog( $H, $path, $program )) {
                    $Program_Paths{ $program } = $real;

lib/Bio/EnsEMBL/Analysis/Programs.pm  view on Meta::CPAN

    }
    _go_home( $H ); # Return to home directory
    
    # Make a list of all missing programs
    foreach my $program (keys %Program_Paths) {
        push( @missing, $program ) unless $Program_Paths{ $program };
    }
    
    # Give informative death message if programs weren't found
    if (@missing) { 
        throw("Unable to locate the following programs as '". (getpwuid($<))[0]. "' on host '". hostname(). "' :\t".
        join ( " --> " , @missing )) ; 
    }
}

# Recursive function which follows links, or tests final destination
sub _is_prog {
    my( $h, $path, $prog ) = @_;

    # Need to split path if $prog not provided
    unless ($prog) {