http://circos.ca/software/download/
wget http://circos.ca/distribution/circos-0.67-7.tgz
tar xvzf circos-0.67-7.tgz
cd circos-0.67-7/bin
ls
circos gddiag list.modules test.modules
which env
/usr/bin/env PS: Edit Shebang in
circos
andgddiag
binary at<extracted circos path>/bin/
to match correct PATH forenv
. In my case, it is#!/usr/bin/env perl
and not default#!/bin/env perl
which perl
/usr/bin/perl
perl -v
v.518.2 #If different, circos works with default perl version shipped with Ubuntu 14.04
- http://circos.ca/software/installation/
- http://circos.ca/tutorials/lessons/configuration/distribution_and_installation/
cd <extracted circos path>/bin/circos/bin
./circos -modules #or
./circos -modules | grep missing
ok 1.29 Carp
ok 0.36 Clone
missing 2.56 Config::General
ok 3.40 Cwd
ok 2.145 Data::Dumper
ok 2.52 Digest::MD5
ok 2.84 File::Basename
ok 3.40 File::Spec::Functions
ok 0.23 File::Temp
ok 1.51 FindBin
missing 0.39 Font::TTF::Font
missing 2.46 GD
missing 0.2 GD::Polyline
ok 2.39 Getopt::Long
ok 1.16 IO::File
ok 0.33 List::MoreUtils
ok 1.27 List::Util
missing 0.01 Math::Bezier
ok 1.998 Math::BigFloat
missing 0.07 Math::Round
missing 0.08 Math::VecStat
ok 1.03 Memoize
ok 1.32 POSIX
missing 1.18 Params::Validate
ok 1.61 Pod::Usage
missing 2 Readonly
missing 2013031301 Regexp::Common
missing 2.63 SVG
missing 1.19 Set::IntSpan
missing 1.6611 Statistics::Basic
ok 2.41 Storable
ok 1.17 Sys::Hostname
ok 2.02 Text::Balanced
missing 0.59 Text::Format
ok 1.9725 Time::HiRes
sudo perl -MCPAN -e shell
cpan shell -- CPAN exploration and modules installation (v2.00) Enter 'h' for help.
cpan[1]>
cpan[2]> install Config::General Font::TTF::Font Math::Bezier Math::Round Math::VecStat Params::Validate Readonly Regexp::Common SVG Set::IntSpan Statistics::Basic Text::Format
#run same command again to check all modules are up-to-date
cpan[3]> install Config::General Font::TTF::Font Math::Bezier Math::Round Math::VecStat Params::Validate Readonly Regexp::Common SVG Set::IntSpan Statistics::Basic Text::Format
cpan[4]>exit
Output of cpan[3] command from above:
Reading
/home/foo/.cpan/Metadata
Database was generated on Fri, 17 Apr 2015 10:41:02 GMT
Config::General is up to date (2.56).
Font::TTF::Font is up to date (0.39).
Math::Bezier is up to date (0.01).
Math::Round is up to date (0.07).
Math::VecStat is up to date (0.08).
Params::Validate is up to date (1.18).
Readonly is up to date (2.00).
Regexp::Common is up to date (2013031301).
SVG is up to date (2.63).
Set::IntSpan is up to date (1.19).
Statistics::Basic is up to date (1.6611).
Text::Format is up to date (0.59).
sudo apt-get install libgd-dev libgd2-xpm-dev libgd-gd2-perl build-essential zlib1g-dev libpng12-dev libjpeg-dev
cd <extracted circos path>/bin/circos/bin
./circos -modules #or
./circos -modules | grep missing
All modules should show
ok
.
- Test
circos
command:
cd <extracted circos path>/bin/circos/example
./run
Test GD installation to make sure your Perl distribution can create graphics and handle True Type fonts.
cd <extracted circos path>/
bin/gddiag
Look at the created gddiag.png in circos../
It should look like: http://www.circos.ca/tutorials/lessons/configuration/png_output/images
END