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guix/gnu/packages/patches/circos-remove-findbin.patch
Roel Janssen 7ff6395100
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.
2020-03-23 11:42:36 +01:00

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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 ----
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