Bio-Genex

 view release on metacpan or  search on metacpan

scripts/configure.pl.in  view on Meta::CPAN

use Getopt::Long;
use File::Basename;
use File::stat;

my $CONFIG_FILE_NAME = 'Config.pm';
my $st_config;

# first we check if we are being run as part of a complete GeneX
# install, or only as an update to Genex.pm
if (cwd() ne 'scripts' && -e "Bio/Genex/$CONFIG_FILE_NAME") {
  $st_config = stat("Bio/Genex/$CONFIG_FILE_NAME");

  # nice trick. we wrote the hash out as a perl module using Data:Dumper,
  # so to recreate it we just 'require' it ;-)
  eval {
    use lib '.';
    require Bio::Genex::Config;
  };
  die "$0: Couldn't load local Config.pm: $@\n"
    if $@;
} elsif (-e "../Bio/Genex/$CONFIG_FILE_NAME") {
  $st_config = stat("../Bio/Genex/$CONFIG_FILE_NAME");

  # nice trick. we wrote the hash out as a perl module using Data:Dumper,
  # so to recreate it we just 'require' it ;-)
  eval {
    use lib '..';
    require Bio::Genex::Config;
  };
  die "$0: Couldn't load local Config.pm: $@\n"
    if $@;
} else {

scripts/configure.pl.in  view on Meta::CPAN

  # we don't want to substitute the configure.pl.in 
  return if /^configure\.pl\.in$/;

  my ($outfile) = $File::Find::name =~ m/^(.*)\.in$/;
  
  # we only want to substitute if the infile has been modified 
  # since we last ran the substitution, or if the config file
  # has been modified
  if (-f $outfile) {
    my $st_out = stat($outfile);
    my $st_in = stat($File::Find::name);

    # First, if the config file is local, check if the config more
    # recent, otherwise check if infile is more recent
    if (!defined $st_config || $st_config->mtime < $st_out->mtime) {
      # has the infile been modified?
      return unless $st_in->mtime > $st_out->mtime;
    }
  }

  open(IN,$File::Find::name) or die "Couldn't open $File::Find::name for reading";

scripts/make_classes.pl  view on Meta::CPAN

    next TARGET  if $CONTROL_ONLY && ! exists $args{controlled};
    next TARGET  if $LINKING_ONLY && ! exists $args{linking};

    my $base = $args{target};
    my $dir = "$ROOT/$base";
    my $file = "$dir/$base.pm";
    die "Couldn't find $file" unless -d $dir;
    if (-e $file) {

      # if the create script is newer than the .pm file redo the class
      my $st_out = stat("$file");
      my $st_in = stat("$CREATE");

      # otherwise check each class's files 
      if ($st_in->mtime < $st_out->mtime) {
	my @files;
	# check the master column2name file
	if (exists $args{controlled}) {
	  push(@files,"$ROOT/ControlledVocab/column2name");	  
	} else {
	  push(@files,"$ROOT/$base/column2name");	  
	}
	# check any supporting column2name files
	if (exists $args{support}) {
	  foreach (@{$args{support}}) {
	    push(@files,"$ROOT/$_/column2name");	  
	  }      
	}
	# go through the files and see if any are more recent
	foreach (@files) {
	  die "Couldn't find $_" unless -e $_;
	  $st_in = stat($_);
	  last if $st_in->mtime > $st_out->mtime;
	}

	# skip this target if none of the files are more recent
	if ($st_in->mtime < $st_out->mtime) {
	  print STDERR "Skipping $file (no change)\n" if $DEBUG; 
	  next TARGET;
	}
      }
    }

scripts/make_classes.pl  view on Meta::CPAN

    $file = "$ROOT/$args{target}" if $args{target} =~ /\.pl$/;
    die "Couldn't find $file" unless -e $file;
    my $base = $args{target};
    $base =~ s|samples/||;
    $base =~ s|scripts/||;
    my $pod  = $base . '.pod';
    
    # we only want to make a new pod file if the infile has been modified 
    # since we last ran created the pod file
    if (-f "$PODROOT/$pod") {
      my $st_out = stat("$PODROOT/$pod");
      my $st_in = stat("$file");
      
      if ($st_in->mtime < $st_out->mtime) {
	print STDERR "Skipping $file (no change)\n" if $DEBUG; 
	next;
      }
    }
    
    my $cmd = "podselect $file  > $pod";
    print STDERR "$cmd\n";
    system("$cmd");

scripts/make_classes.pl  view on Meta::CPAN

    $file = "$ROOT/$args{target}" if $args{target} =~ /^samples/;
    my $base = $args{target};
    $base =~ s|samples/||;
    $base =~ s|scripts/||;
    my $pod  = $base . '.pod';
    my $html = $base . '.html';
    
    # we only want to make a new html file if the pod file has been changed
    # since we last ran created the html file
    if (-f "$HTMLROOT/$html") {
      my $st_out = stat("$HTMLROOT/$html");
      my $st_in = stat("$PODROOT/$pod");
      
      if ($st_in->mtime < $st_out->mtime) {
	print STDERR "Skipping $HTMLROOT/$html (no change)\n" if $DEBUG;
	next;
      }
    }
    
    my $cmd = "pod2html $p2h_args --infile=$pod  --outfile=$HTMLROOT/$html";
    print STDERR "$cmd\n";
    system("$cmd");