Install circos on ubuntu 14.04 LTS

circos_install_ubuntu_1404.md

Download Circos:

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 and gddiag binary at <extracted circos path>/bin/ to match correct PATH for env. In my case, it is #!/usr/bin/env perl and not default #!/bin/env perl

Get dependencies:

which perl

/usr/bin/perl

perl -v

v.518.2 #If different, circos works with default perl version shipped with Ubuntu 14.04

Install perl modules:

• 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

For non-GD modules, install via cpan prompt:

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).

Install GD and GD::Polyline pacakges using libgd-gd2... packages via apt-get command:

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:

• 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

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