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|
=pod
=head1 NAME
Circos::Modules - module checking for Circos
=head1 SYNOPSIS
This module is not meant to be used directly.
=head1 DESCRIPTION
Circos is an application for the generation of publication-quality,
circularly composited renditions of genomic data and related
annotations.
Circos is particularly suited for visualizing alignments, conservation
and intra and inter-chromosomal relationships. However, Circos can be
used to plot any kind of 2D data in a circular layout - its use is not
limited to genomics. Circos' use of lines to relate position pairs
(ribbons add a thickness parameter to each end) is effective to
display relationships between objects or positions on one or more
scales.
All documentation is in the form of tutorials at L<http://www.circos.ca>.
=cut
# -------------------------------------------------------------------
use strict;
use warnings;
use base 'Exporter';
our @EXPORT = qw(
module_check
);
our @modules = (
"Carp qw(carp confess croak)",
"Clone",
"Config::General 2.54",
"Cwd",
"Data::Dumper",
"Digest::MD5 qw(md5_hex)",
"File::Basename",
"File::Spec::Functions",
"File::Temp qw(tempdir)",
"FindBin",
"Font::TTF::Font",
"GD",
"GD::Polyline",
"Getopt::Long",
"IO::File",
"List::MoreUtils qw(uniq)",
"List::Util qw(max min)",
"Math::Bezier",
"Math::BigFloat",
"Math::Round qw(round nearest)",
"Math::VecStat qw(sum average)",
"Memoize",
"POSIX qw(atan)",
"Params::Validate qw(:all)",
"Pod::Usage",
"Readonly",
"Regexp::Common qw(number)",
"Set::IntSpan 1.16 qw(map_set)",
"Statistics::Basic qw(average stddev)",
"Storable",
"SVG",
"Sys::Hostname",
"Text::Balanced",
"Text::Format",
"Time::HiRes qw(gettimeofday tv_interval)",
);
# Checks whether required modules (names found in @modules) are installed.
#
# Returns 0 if some modules are missing or report (using -modules) was generated
# Returns 1 if all modules are installed
sub check_modules {
my @missing;
for my $m (@modules) {
my ($root) = split(" ",$m);
if(eval "use $m; 1") {
#
} else {
push @missing, [$m,$@];
}
}
if(grep($_ =~ /-modules?/i, @ARGV)) {
for my $m (sort @modules) {
my $is_missing = grep($_->[0] eq $m, @missing) || 0;
$m =~ s/ .*//;
my $version = "";
if(! $is_missing) {
eval { my $ver_str = $m . "::VERSION" ; $version = eval "\$$ver_str" };
$version ||= "?";
}
printf("%s %10s %s\n", $is_missing ? "missing" : "ok",$version,$m);
}
return 0;
}
if(@missing) {
printf("\n*** REQUIRED MODULE(S) MISSING OR OUT-OF-DATE ***\n\n");
printf("You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial\n\nhttp://www.circos.ca/documentation/tutorials/configuration/perl_and_modules\n\n");
for my $pair (sort @missing) {
my ($m,$error) = @$pair;
$m =~ s/ .*//;
printf("missing %s\n",$m);
$error =~ s/\n//g;
$error =~ s/BEGIN failed.*//;
printf(" error %s\n",$error);
}
return 0;
}
return 1;
}
|
