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.
This commit is contained in:
Roel Janssen
parent
591faabd8c
commit
7ff6395100
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@ -777,6 +777,7 @@ dist_patch_DATA = \
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%D%/packages/patches/calibre-remove-test-unrar.patch \
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%D%/packages/patches/casync-renameat2-declaration.patch \
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%D%/packages/patches/catdoc-CVE-2017-11110.patch \
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%D%/packages/patches/circos-remove-findbin.patch \
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%D%/packages/patches/cdparanoia-fpic.patch \
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%D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch \
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%D%/packages/patches/ceph-disable-cpu-optimizations.patch \
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@ -0,0 +1,544 @@
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This patch was created by Roel Janssen <roel@gnu.org>.
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Circos uses paths relative to the "circos" script to find its Perl modules.
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This patch removes that mechanism, and instead expects the 'Circos' modules
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to be available in the global Perl path.
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diff -crB circos-0.69-6/bin/circos circos-0.69-6-new/bin/circos
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*** circos-0.69-6/bin/circos 2016-02-19 01:42:59.000000000 +0100
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--- circos-0.69-6-new/bin/circos 2018-01-12 09:59:25.662731269 +0100
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***************
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*** 474,486 ****
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use strict;
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use warnings;
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- use FindBin;
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use Getopt::Long qw(:config pass_through posix_default auto_abbrev);
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use Pod::Usage;
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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use Circos;
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use Cwd;
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--- 474,482 ----
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diff -crB circos-0.69-6/lib/Circos/Colors.pm circos-0.69-6-new/lib/Circos/Colors.pm
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*** circos-0.69-6/lib/Circos/Colors.pm 2015-03-17 01:25:43.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Colors.pm 2018-01-12 10:10:39.174797379 +0100
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***************
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*** 49,55 ****
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use Carp qw( carp confess croak );
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use Digest::MD5 qw(md5_hex);
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- use FindBin;
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use File::Basename;
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use File::Spec::Functions;
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use File::Temp qw(tempdir);
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--- 49,54 ----
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***************
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*** 65,74 ****
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#use Time::HiRes qw(gettimeofday tv_interval);
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#use List::Util qw( max min );
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use POSIX qw(pow);
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use Circos::Configuration;
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--- 64,69 ----
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diff -crB circos-0.69-6/lib/Circos/Configuration.pm circos-0.69-6-new/lib/Circos/Configuration.pm
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*** circos-0.69-6/lib/Circos/Configuration.pm 2015-03-17 22:11:01.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Configuration.pm 2018-01-12 10:11:41.064008273 +0100
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***************
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*** 59,68 ****
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use Params::Validate qw(:all);
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use List::MoreUtils qw(uniq);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Constants;
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use Circos::Debug;
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use Circos::Utils;
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--- 59,64 ----
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diff -crB circos-0.69-6/lib/Circos/DataPoint.pm circos-0.69-6-new/lib/Circos/DataPoint.pm
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*** circos-0.69-6/lib/Circos/DataPoint.pm 2014-05-12 18:20:19.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/DataPoint.pm 2018-01-12 10:11:54.888270731 +0100
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***************
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*** 38,51 ****
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use Carp qw( carp confess croak );
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use Data::Dumper;
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- use FindBin;
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use GD::Image;
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration; # qw(%CONF $DIMS);
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use Circos::Constants;
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use Circos::Debug;
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--- 38,46 ----
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diff -crB circos-0.69-6/lib/Circos/Debug.pm circos-0.69-6-new/lib/Circos/Debug.pm
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*** circos-0.69-6/lib/Circos/Debug.pm 2015-03-24 01:26:13.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Debug.pm 2018-01-12 10:12:07.192502006 +0100
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***************
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*** 63,75 ****
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use Carp qw( carp confess croak );
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use Data::Dumper;
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- use FindBin;
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use Memoize;
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use List::MoreUtils qw(uniq);
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use Time::HiRes qw(gettimeofday tv_interval);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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use Circos::Constants;
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--- 63,71 ----
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diff -crB circos-0.69-6/lib/Circos/Division.pm circos-0.69-6-new/lib/Circos/Division.pm
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*** circos-0.69-6/lib/Circos/Division.pm 2015-11-17 00:55:58.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Division.pm 2018-01-12 10:12:21.544769084 +0100
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***************
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*** 37,52 ****
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our @EXPORT = qw();
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use Carp qw( carp confess croak );
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- use FindBin;
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use GD;
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use Math::Round;
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use List::MoreUtils qw(uniq);
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Constants;
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use Circos::Debug;
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--- 37,47 ----
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diff -crB circos-0.69-6/lib/Circos/Error.pm circos-0.69-6-new/lib/Circos/Error.pm
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*** circos-0.69-6/lib/Circos/Error.pm 2015-03-17 22:46:36.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Error.pm 2018-01-12 10:12:32.472970548 +0100
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***************
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*** 44,53 ****
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use Params::Validate;
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use Text::Format;
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Constants;
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use Circos::Debug;
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use Circos::Utils;
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--- 44,49 ----
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diff -crB circos-0.69-6/lib/Circos/Expression.pm circos-0.69-6-new/lib/Circos/Expression.pm
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*** circos-0.69-6/lib/Circos/Expression.pm 2015-11-30 23:49:36.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Expression.pm 2018-01-12 10:12:41.953144015 +0100
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***************
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*** 39,55 ****
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use Carp qw( carp confess croak );
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use Data::Dumper;
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- use FindBin;
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use Params::Validate qw(:all);
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use Math::Round;
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use Math::VecStat qw(average);
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use List::Util qw(min max);
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use Text::Balanced qw(extract_bracketed);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Constants;
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use Circos::Debug;
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--- 39,50 ----
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diff -crB circos-0.69-6/lib/Circos/Font.pm circos-0.69-6-new/lib/Circos/Font.pm
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*** circos-0.69-6/lib/Circos/Font.pm 2014-05-12 18:20:19.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Font.pm 2018-01-12 10:12:51.657320357 +0100
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***************
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*** 45,59 ****
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);
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use Carp qw( carp confess croak );
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- use FindBin;
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use GD::Image;
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use Font::TTF::Font;
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
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use Circos::Constants;
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use Circos::Colors;
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--- 45,54 ----
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diff -crB circos-0.69-6/lib/Circos/Geometry.pm circos-0.69-6-new/lib/Circos/Geometry.pm
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*** circos-0.69-6/lib/Circos/Geometry.pm 2014-05-12 18:20:19.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Geometry.pm 2018-01-12 10:12:58.961452282 +0100
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***************
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*** 41,54 ****
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);
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use Carp qw( carp confess croak );
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- use FindBin;
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use GD::Image;
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration; # qw(%CONF $DIMS fetch_conf);
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use Circos::Constants;
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use Circos::Debug;
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--- 41,49 ----
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diff -crB circos-0.69-6/lib/Circos/Heatmap.pm circos-0.69-6-new/lib/Circos/Heatmap.pm
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*** circos-0.69-6/lib/Circos/Heatmap.pm 2016-03-30 22:08:12.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Heatmap.pm 2018-01-12 10:13:09.953649538 +0100
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***************
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*** 24,40 ****
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use Carp qw( carp confess croak );
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use Clone;
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use Data::Dumper;
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- use FindBin;
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use GD::Image;
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use Math::VecStat qw(min max);
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use Params::Validate qw(:all);
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use List::MoreUtils qw(uniq);
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use Regexp::Common qw(number);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Constants;
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use Circos::Colors;
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--- 24,35 ----
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diff -crB circos-0.69-6/lib/Circos/Ideogram.pm circos-0.69-6-new/lib/Circos/Ideogram.pm
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*** circos-0.69-6/lib/Circos/Ideogram.pm 2015-11-17 01:18:53.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/Ideogram.pm 2018-01-12 10:13:22.045864798 +0100
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***************
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*** 40,46 ****
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use Carp qw( carp confess croak );
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use Cwd;
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- use FindBin;
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use File::Spec::Functions;
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use Math::Round;
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use Math::VecStat qw(max);
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--- 40,45 ----
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***************
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*** 50,59 ****
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use POSIX qw(floor ceil);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Constants;
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use Circos::Debug;
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--- 49,54 ----
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diff -crB circos-0.69-6/lib/Circos/Image.pm circos-0.69-6-new/lib/Circos/Image.pm
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*** circos-0.69-6/lib/Circos/Image.pm 2014-05-12 18:20:19.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Image.pm 2018-01-12 10:13:31.094024696 +0100
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***************
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*** 45,58 ****
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);
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use Carp qw( carp confess croak );
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- use FindBin;
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use GD::Image;
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Colors;
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use Circos::Constants;
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--- 45,53 ----
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diff -crB circos-0.69-6/lib/Circos/IO.pm circos-0.69-6-new/lib/Circos/IO.pm
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*** circos-0.69-6/lib/Circos/IO.pm 2015-12-03 05:51:11.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/IO.pm 2018-01-12 10:13:41.686210640 +0100
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***************
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*** 39,45 ****
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use Carp qw( carp confess croak );
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use Storable qw(dclone);
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use Cwd;
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- use FindBin;
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use Data::Dumper;
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use File::Spec::Functions;
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use Math::Round;
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--- 39,44 ----
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***************
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*** 49,58 ****
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use POSIX qw(floor ceil);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Constants;
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use Circos::Colors;
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use Circos::Configuration;
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--- 48,53 ----
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diff -crB circos-0.69-6/lib/Circos/Karyotype.pm circos-0.69-6-new/lib/Circos/Karyotype.pm
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*** circos-0.69-6/lib/Circos/Karyotype.pm 2014-09-09 00:15:58.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Karyotype.pm 2018-01-12 10:13:53.318413330 +0100
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***************
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*** 38,44 ****
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use Carp qw( carp confess croak );
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use Cwd;
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- use FindBin;
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use Math::Round;
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use Math::VecStat qw(max);
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use Params::Validate qw(:all);
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--- 38,43 ----
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***************
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*** 48,57 ****
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#use Regexp::Common qw(number);
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#use POSIX qw(floor ceil);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Constants;
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use Circos::Debug;
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--- 47,52 ----
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diff -crB circos-0.69-6/lib/Circos/PNG.pm circos-0.69-6-new/lib/Circos/PNG.pm
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*** circos-0.69-6/lib/Circos/PNG.pm 2014-09-17 05:33:06.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/PNG.pm 2018-01-12 10:14:31.011059637 +0100
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***************
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*** 37,51 ****
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our @EXPORT = qw();
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use Carp qw( carp confess croak );
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- use FindBin;
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use GD;
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use Math::VecStat qw(min max);
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use Params::Validate qw(:all);
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Colors;
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use Circos::Constants;
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--- 37,46 ----
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diff -crB circos-0.69-6/lib/Circos/Rule.pm circos-0.69-6-new/lib/Circos/Rule.pm
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*** circos-0.69-6/lib/Circos/Rule.pm 2014-10-02 01:14:25.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Rule.pm 2018-01-12 10:14:38.195181067 +0100
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***************
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*** 38,51 ****
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use Carp qw( carp confess croak );
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use Data::Dumper;
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- use FindBin;
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use GD::Image;
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use Params::Validate qw(:all);
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|
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- use lib "$FindBin::RealBin";
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- use lib "$FindBin::RealBin/../lib";
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration; # qw(%CONF $DIMS);
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use Circos::Constants;
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use Circos::DataPoint;
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--- 38,46 ----
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diff -crB circos-0.69-6/lib/Circos/SVG.pm circos-0.69-6-new/lib/Circos/SVG.pm
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*** circos-0.69-6/lib/Circos/SVG.pm 2015-11-30 23:23:52.000000000 +0100
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--- circos-0.69-6-new/lib/Circos/SVG.pm 2018-01-12 10:14:47.803342631 +0100
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***************
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*** 26,39 ****
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);
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use Carp qw( carp confess croak );
|
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- use FindBin;
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use GD::Image;
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use Params::Validate qw(:all);
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|
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- use lib "$FindBin::RealBin";
|
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- use lib "$FindBin::RealBin/../lib";
|
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- use lib "$FindBin::RealBin/lib";
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-
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use Circos::Configuration;
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use Circos::Colors;
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use Circos::Constants;
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--- 26,34 ----
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diff -crB circos-0.69-6/lib/Circos/Text.pm circos-0.69-6-new/lib/Circos/Text.pm
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*** circos-0.69-6/lib/Circos/Text.pm 2014-05-12 18:20:19.000000000 +0200
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--- circos-0.69-6-new/lib/Circos/Text.pm 2018-01-12 10:14:57.083497772 +0100
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***************
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*** 42,55 ****
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);
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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 ----
|
||||
|
|
@ -52,6 +52,7 @@
|
|||
#:use-module (gnu packages base)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages freedesktop)
|
||||
#:use-module (gnu packages gd)
|
||||
#:use-module (gnu packages less)
|
||||
#:use-module (gnu packages ncurses)
|
||||
#:use-module (gnu packages perl-check)
|
||||
|
|
@ -870,6 +871,101 @@ the Carp.pm module doesn't help.")
|
|||
;; Either GPLv2 or the "Artistic" license.
|
||||
(license (list gpl2 artistic2.0))))
|
||||
|
||||
(define-public circos
|
||||
(package
|
||||
(name "circos")
|
||||
(version "0.69-9")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"http://circos.ca/distribution/circos-" version ".tgz"))
|
||||
(sha256
|
||||
(base32 "1ll9yxbk0v64813np0qz6h8bc53qlnhg9y1053b57xgkxgmxgn1l"))
|
||||
(patches (list (search-patch "circos-remove-findbin.patch")))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(delete 'build)
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let* ((out (assoc-ref outputs "out"))
|
||||
(bin (string-append out "/bin"))
|
||||
(datapath (string-append out "/share/Circos"))
|
||||
(error (string-append out "/share/Circos/error"))
|
||||
(fonts (string-append out "/share/Circos/fonts"))
|
||||
(data (string-append out "/share/Circos/data"))
|
||||
(tiles (string-append out "/share/Circos/tiles"))
|
||||
(etc (string-append out "/share/Circos/etc"))
|
||||
(lib (string-append out "/lib/perl5/site_perl/"
|
||||
,(package-version perl)))
|
||||
(install-directory (lambda (source target)
|
||||
(mkdir-p target)
|
||||
(copy-recursively source target))))
|
||||
;; Circos looks into a relative path for its configuration
|
||||
;; files. We need to provide an absolute path towards the
|
||||
;; corresponding paths in the store.
|
||||
(substitute* '("bin/circos" "etc/colors_fonts_patterns.conf"
|
||||
"etc/gddiag.conf" "etc/brewer.conf" "README")
|
||||
(("<<include etc") (string-append "<<include " etc)))
|
||||
(substitute* '("etc/colors.conf" "etc/image.black.conf"
|
||||
"etc/patterns.conf" "etc/image.conf")
|
||||
(("<<include ") (string-append "<<include " etc "/")))
|
||||
(substitute* '("etc/fonts.conf" "fonts/README.fonts")
|
||||
(("= fonts") (string-append "= " fonts)))
|
||||
(substitute* "etc/patterns.conf"
|
||||
(("= tiles") (string-append "= " tiles)))
|
||||
(substitute* "lib/Circos/Error.pm"
|
||||
(("error/configuration.missing.txt")
|
||||
(string-append error "/configuration.missing.txt")))
|
||||
(substitute* "etc/housekeeping.conf"
|
||||
(("# data_path = /home/martink/circos-tutorials ")
|
||||
(string-append "data_path = " datapath)))
|
||||
(substitute* "lib/Circos/Configuration.pm"
|
||||
(("my @possibilities = \\(")
|
||||
(string-append "my @possibilities = ("
|
||||
"catfile( \"" datapath "\", $arg ), "
|
||||
"catfile( \"" etc "\", $arg ), "
|
||||
"catfile( \"" etc "/tracks\", $arg ), ")))
|
||||
(for-each install-directory
|
||||
(list "error" "fonts" "data" "tiles" "etc" "lib")
|
||||
(list error fonts data tiles etc lib))
|
||||
(install-file "bin/circos" bin)
|
||||
#t))))))
|
||||
(propagated-inputs
|
||||
`(("perl" ,perl)
|
||||
("perl-carp" ,perl-carp)
|
||||
("perl-clone" ,perl-clone)
|
||||
("perl-config-general" ,perl-config-general)
|
||||
("perl-digest-md5" ,perl-digest-md5)
|
||||
("perl-file-temp" ,perl-file-temp)
|
||||
("perl-font-ttf" ,perl-font-ttf)
|
||||
("perl-gd" ,perl-gd)
|
||||
("perl-getopt-long" ,perl-getopt-long)
|
||||
("perl-list-allutils" ,perl-list-allutils)
|
||||
("perl-math-bezier" ,perl-math-bezier)
|
||||
("perl-math-round" ,perl-math-round)
|
||||
("perl-math-vecstat" ,perl-math-vecstat)
|
||||
("perl-memoize" ,perl-memoize)
|
||||
("perl-number-format" ,perl-number-format)
|
||||
("perl-params-validate" ,perl-params-validate)
|
||||
("perl-readonly" ,perl-readonly)
|
||||
("perl-regexp-common" ,perl-regexp-common)
|
||||
("perl-set-intspan" ,perl-set-intspan)
|
||||
("perl-statistics-basic" ,perl-statistics-basic)
|
||||
("perl-svg" ,perl-svg)
|
||||
("perl-text-balanced" ,perl-text-balanced)
|
||||
("perl-text-format" ,perl-text-format)
|
||||
("perl-time-hires" ,perl-time-hires)))
|
||||
(home-page "http://circos.ca/")
|
||||
(synopsis "Generation of circularly composited renditions")
|
||||
(description
|
||||
"Circos is a program for the generation of publication-quality, circularly
|
||||
composited renditions of genomic data and related annotations.")
|
||||
(license gpl2+)))
|
||||
|
||||
(define-public perl-class-accessor
|
||||
(package
|
||||
(name "perl-class-accessor")
|
||||
|
|
|
|||
Loading…
Reference in New Issue