gnu: Add circos.

* gnu/local.mk: Register circos-remove-findbin.patch.
* gnu/packages/patches/circos-remove-findbin.patch: New file.
* gnu/packages/perl.scm: New variable.

1 files changed, 544 insertions, 0 deletions

diff --git a/gnu/packages/patches/circos-remove-findbin.patch b/gnu/packages/patches/circos-remove-findbin.patch
new file mode 100644
index 0000000000..5675172e5d
--- /dev/null
+++ b/gnu/packages/patches/circos-remove-findbin.patch
@@ -0,0 +1,544 @@
+This patch was created by Roel Janssen <roel@gnu.org>.
+
+Circos uses paths relative to the "circos" script to find its Perl modules.
+This patch removes that mechanism, and instead expects the 'Circos' modules
+to be available in the global Perl path.
+ 
+diff -crB circos-0.69-6/bin/circos circos-0.69-6-new/bin/circos
+*** circos-0.69-6/bin/circos	2016-02-19 01:42:59.000000000 +0100
+--- circos-0.69-6-new/bin/circos	2018-01-12 09:59:25.662731269 +0100
+***************
+*** 474,486 ****
+  
+  use strict;
+  use warnings;
+- use FindBin;
+  use Getopt::Long qw(:config pass_through posix_default auto_abbrev);
+  use Pod::Usage;
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+  use Circos;
+  
+  use Cwd;
+--- 474,482 ----
+diff -crB circos-0.69-6/lib/Circos/Colors.pm circos-0.69-6-new/lib/Circos/Colors.pm
+*** circos-0.69-6/lib/Circos/Colors.pm	2015-03-17 01:25:43.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Colors.pm	2018-01-12 10:10:39.174797379 +0100
+***************
+*** 49,55 ****
+  
+  use Carp qw( carp confess croak );
+  use Digest::MD5 qw(md5_hex);
+- use FindBin;
+  use File::Basename;
+  use File::Spec::Functions;
+  use File::Temp qw(tempdir);
+--- 49,54 ----
+***************
+*** 65,74 ****
+  #use Time::HiRes qw(gettimeofday tv_interval);
+  #use List::Util qw( max min );
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use POSIX qw(pow);
+
+  use Circos::Configuration;
+--- 64,69 ----
+diff -crB circos-0.69-6/lib/Circos/Configuration.pm circos-0.69-6-new/lib/Circos/Configuration.pm
+*** circos-0.69-6/lib/Circos/Configuration.pm	2015-03-17 22:11:01.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Configuration.pm	2018-01-12 10:11:41.064008273 +0100
+***************
+*** 59,68 ****
+  use Params::Validate qw(:all);
+  use List::MoreUtils qw(uniq);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Constants;
+  use Circos::Debug;
+  use Circos::Utils;
+--- 59,64 ----
+diff -crB circos-0.69-6/lib/Circos/DataPoint.pm circos-0.69-6-new/lib/Circos/DataPoint.pm
+*** circos-0.69-6/lib/Circos/DataPoint.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/DataPoint.pm	2018-01-12 10:11:54.888270731 +0100
+***************
+*** 38,51 ****
+  
+  use Carp qw( carp confess croak );
+  use Data::Dumper;
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+  use Circos::Debug;
+--- 38,46 ----
+diff -crB circos-0.69-6/lib/Circos/Debug.pm circos-0.69-6-new/lib/Circos/Debug.pm
+*** circos-0.69-6/lib/Circos/Debug.pm	2015-03-24 01:26:13.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Debug.pm	2018-01-12 10:12:07.192502006 +0100
+***************
+*** 63,75 ****
+  
+  use Carp qw( carp confess croak );
+  use Data::Dumper;
+- use FindBin;
+  use Memoize;
+  use List::MoreUtils qw(uniq);
+  use Time::HiRes qw(gettimeofday tv_interval);
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+  
+  use Circos::Constants;
+  
+--- 63,71 ----
+diff -crB circos-0.69-6/lib/Circos/Division.pm circos-0.69-6-new/lib/Circos/Division.pm
+*** circos-0.69-6/lib/Circos/Division.pm	2015-11-17 00:55:58.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Division.pm	2018-01-12 10:12:21.544769084 +0100
+***************
+*** 37,52 ****
+  our @EXPORT = qw();
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD;
+  use Math::Round;
+  use List::MoreUtils qw(uniq);
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Constants;
+  use Circos::Debug;
+--- 37,47 ----
+diff -crB circos-0.69-6/lib/Circos/Error.pm circos-0.69-6-new/lib/Circos/Error.pm
+*** circos-0.69-6/lib/Circos/Error.pm	2015-03-17 22:46:36.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Error.pm	2018-01-12 10:12:32.472970548 +0100
+***************
+*** 44,53 ****
+  use Params::Validate;
+  use Text::Format;
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Constants;
+  use Circos::Debug;
+  use Circos::Utils;
+--- 44,49 ----
+diff -crB circos-0.69-6/lib/Circos/Expression.pm circos-0.69-6-new/lib/Circos/Expression.pm
+*** circos-0.69-6/lib/Circos/Expression.pm	2015-11-30 23:49:36.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Expression.pm	2018-01-12 10:12:41.953144015 +0100
+***************
+*** 39,55 ****
+  
+  use Carp qw( carp confess croak );
+  use Data::Dumper;
+- use FindBin;
+  use Params::Validate qw(:all);
+  use Math::Round;
+  use Math::VecStat qw(average);
+  use List::Util qw(min max);
+  use Text::Balanced qw(extract_bracketed);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Constants;
+  use Circos::Debug;
+--- 39,50 ----
+diff -crB circos-0.69-6/lib/Circos/Font.pm circos-0.69-6-new/lib/Circos/Font.pm
+*** circos-0.69-6/lib/Circos/Font.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Font.pm	2018-01-12 10:12:51.657320357 +0100
+***************
+*** 45,59 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Font::TTF::Font;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
+  use Circos::Constants;
+  use Circos::Colors;
+--- 45,54 ----
+diff -crB circos-0.69-6/lib/Circos/Geometry.pm circos-0.69-6-new/lib/Circos/Geometry.pm
+*** circos-0.69-6/lib/Circos/Geometry.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Geometry.pm	2018-01-12 10:12:58.961452282 +0100
+***************
+*** 41,54 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
+  use Circos::Constants;
+  use Circos::Debug;
+--- 41,49 ----
+diff -crB circos-0.69-6/lib/Circos/Heatmap.pm circos-0.69-6-new/lib/Circos/Heatmap.pm
+*** circos-0.69-6/lib/Circos/Heatmap.pm	2016-03-30 22:08:12.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Heatmap.pm	2018-01-12 10:13:09.953649538 +0100
+***************
+*** 24,40 ****
+  use Carp qw( carp confess croak );
+  use Clone;
+  use Data::Dumper;
+- use FindBin;
+  use GD::Image;
+  use Math::VecStat qw(min max);
+  use Params::Validate qw(:all);
+  use List::MoreUtils qw(uniq);
+  use Regexp::Common qw(number);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Constants;
+  use Circos::Colors;
+--- 24,35 ----
+diff -crB circos-0.69-6/lib/Circos/Ideogram.pm circos-0.69-6-new/lib/Circos/Ideogram.pm
+*** circos-0.69-6/lib/Circos/Ideogram.pm	2015-11-17 01:18:53.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/Ideogram.pm	2018-01-12 10:13:22.045864798 +0100
+***************
+*** 40,46 ****
+  
+  use Carp qw( carp confess croak );
+  use Cwd;
+- use FindBin;
+  use File::Spec::Functions;
+  use Math::Round;
+  use Math::VecStat qw(max);
+--- 40,45 ----
+***************
+*** 50,59 ****
+  
+  use POSIX qw(floor ceil);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Constants;
+  use Circos::Debug;
+--- 49,54 ----
+diff -crB circos-0.69-6/lib/Circos/Image.pm circos-0.69-6-new/lib/Circos/Image.pm
+*** circos-0.69-6/lib/Circos/Image.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Image.pm	2018-01-12 10:13:31.094024696 +0100
+***************
+*** 45,58 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; 
+  use Circos::Colors;
+  use Circos::Constants;
+--- 45,53 ----
+diff -crB circos-0.69-6/lib/Circos/IO.pm circos-0.69-6-new/lib/Circos/IO.pm
+*** circos-0.69-6/lib/Circos/IO.pm	2015-12-03 05:51:11.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/IO.pm	2018-01-12 10:13:41.686210640 +0100
+***************
+*** 39,45 ****
+  use Carp qw( carp confess croak );
+  use Storable qw(dclone);
+  use Cwd;
+- use FindBin;
+  use Data::Dumper;
+  use File::Spec::Functions;
+  use Math::Round;
+--- 39,44 ----
+***************
+*** 49,58 ****
+  
+  use POSIX qw(floor ceil);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Constants;
+  use Circos::Colors;
+  use Circos::Configuration;
+--- 48,53 ----
+diff -crB circos-0.69-6/lib/Circos/Karyotype.pm circos-0.69-6-new/lib/Circos/Karyotype.pm
+*** circos-0.69-6/lib/Circos/Karyotype.pm	2014-09-09 00:15:58.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Karyotype.pm	2018-01-12 10:13:53.318413330 +0100
+***************
+*** 38,44 ****
+  
+  use Carp qw( carp confess croak );
+  use Cwd;
+- use FindBin;
+  use Math::Round;
+  use Math::VecStat qw(max);
+  use Params::Validate qw(:all);
+--- 38,43 ----
+***************
+*** 48,57 ****
+  #use Regexp::Common qw(number);
+  #use POSIX qw(floor ceil);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Constants;
+  use Circos::Debug;
+--- 47,52 ----
+diff -crB circos-0.69-6/lib/Circos/PNG.pm circos-0.69-6-new/lib/Circos/PNG.pm
+*** circos-0.69-6/lib/Circos/PNG.pm	2014-09-17 05:33:06.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/PNG.pm	2018-01-12 10:14:31.011059637 +0100
+***************
+*** 37,51 ****
+  our @EXPORT = qw();
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD;
+  use Math::VecStat qw(min max);
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Colors;
+  use Circos::Constants;
+--- 37,46 ----
+diff -crB circos-0.69-6/lib/Circos/Rule.pm circos-0.69-6-new/lib/Circos/Rule.pm
+*** circos-0.69-6/lib/Circos/Rule.pm	2014-10-02 01:14:25.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Rule.pm	2018-01-12 10:14:38.195181067 +0100
+***************
+*** 38,51 ****
+  
+  use Carp qw( carp confess croak );
+  use Data::Dumper;
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+  use Circos::DataPoint;
+--- 38,46 ----
+diff -crB circos-0.69-6/lib/Circos/SVG.pm circos-0.69-6-new/lib/Circos/SVG.pm
+*** circos-0.69-6/lib/Circos/SVG.pm	2015-11-30 23:23:52.000000000 +0100
+--- circos-0.69-6-new/lib/Circos/SVG.pm	2018-01-12 10:14:47.803342631 +0100
+***************
+*** 26,39 ****
+  							 );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  use Circos::Colors;
+  use Circos::Constants;
+--- 26,34 ----
+diff -crB circos-0.69-6/lib/Circos/Text.pm circos-0.69-6-new/lib/Circos/Text.pm
+*** circos-0.69-6/lib/Circos/Text.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Text.pm	2018-01-12 10:14:57.083497772 +0100
+***************
+*** 42,55 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+  use Circos::Colors;
+--- 42,50 ----
+diff -crB circos-0.69-6/lib/Circos/Track/Highlight.pm circos-0.69-6-new/lib/Circos/Track/Highlight.pm
+*** circos-0.69-6/lib/Circos/Track/Highlight.pm	2014-10-01 00:43:27.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Track/Highlight.pm	2018-01-12 10:15:06.795659206 +0100
+***************
+*** 37,50 ****
+  our @EXPORT = qw();
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+  #use Circos::Colors;
+--- 37,45 ----
+diff -crB circos-0.69-6/lib/Circos/Track/Link.pm circos-0.69-6-new/lib/Circos/Track/Link.pm
+*** circos-0.69-6/lib/Circos/Track/Link.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Track/Link.pm	2018-01-12 10:15:17.387834198 +0100
+***************
+*** 37,50 ****
+  our @EXPORT = qw();
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD::Image;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+  #use Circos::Colors;
+--- 37,45 ----
+diff -crB circos-0.69-6/lib/Circos/Track.pm circos-0.69-6-new/lib/Circos/Track.pm
+*** circos-0.69-6/lib/Circos/Track.pm	2014-09-16 05:31:46.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Track.pm	2018-01-12 10:15:29.628035063 +0100
+***************
+*** 41,56 ****
+  
+  use Carp qw( carp confess croak );
+  use Data::Dumper;
+- use FindBin;
+  use GD::Image;
+  use List::MoreUtils qw(uniq);
+  use Math::VecStat qw(min max);
+  use Params::Validate qw(:all);
+  use Regexp::Common;
+  use Statistics::Basic qw(average stddev);
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+  
+  use Circos::Configuration; # qw(%CONF $DIMS);
+  use Circos::Constants;
+--- 41,52 ----
+diff -crB circos-0.69-6/lib/Circos/Unit.pm circos-0.69-6-new/lib/Circos/Unit.pm
+*** circos-0.69-6/lib/Circos/Unit.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Unit.pm	2018-01-12 10:15:37.892169871 +0100
+***************
+*** 46,60 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use Data::Dumper;
+  use Params::Validate qw(:all);
+  use Regexp::Common qw(number);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration qw(%CONF $DIMS);
+  use Circos::Constants;
+  use Circos::Debug;
+--- 46,55 ----
+diff -crB circos-0.69-6/lib/Circos/URL.pm circos-0.69-6-new/lib/Circos/URL.pm
+*** circos-0.69-6/lib/Circos/URL.pm	2014-05-12 18:20:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/URL.pm	2018-01-12 10:15:46.092303006 +0100
+***************
+*** 39,52 ****
+  );
+  
+  use Carp qw( carp confess croak );
+- use FindBin;
+  use GD;
+  use Params::Validate qw(:all);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Configuration;
+  #use Circos::Colors;
+  use Circos::Constants;
+--- 39,47 ----
+diff -crB circos-0.69-6/lib/Circos/Utils.pm circos-0.69-6-new/lib/Circos/Utils.pm
+*** circos-0.69-6/lib/Circos/Utils.pm	2014-10-01 21:36:19.000000000 +0200
+--- circos-0.69-6-new/lib/Circos/Utils.pm	2018-01-12 10:16:11.576712858 +0100
+***************
+*** 105,114 ****
+  
+  use POSIX qw(floor ceil);
+  
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+- 
+  use Circos::Constants;
+  use Circos::Debug;
+  use Circos::Error;
+--- 105,110 ----
+diff -crB circos-0.69-6/lib/Circos.pm circos-0.69-6-new/lib/Circos.pm
+*** circos-0.69-6/lib/Circos.pm	2016-06-25 00:19:27.000000000 +0200
+--- circos-0.69-6-new/lib/Circos.pm	2018-01-12 10:16:35.801097176 +0100
+***************
+*** 49,57 ****
+  
+  use strict;
+  use warnings;
+- use lib "$FindBin::RealBin";
+- use lib "$FindBin::RealBin/../lib";
+- use lib "$FindBin::RealBin/lib";
+  
+  BEGIN {
+  	require Circos::Modules;
+--- 49,54 ----