====== Circos ======
Circos is a software package for visualizing data and information a circular layout.

===== Information =====

  * Version: 0.69-9
  * Added: July, 2014
  * Updated: September, 2020
  * Link: http://circos.ca/

===== Usage =====

See versions of circos which are available:
<code>$ module avail circos</code>

Load one version into your environment and run it:
<code>$ module load circos/0.69-9
$ circos</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://circos.ca/distribution/circos-0.69-9.tgz
$ tar zxf circos-0.69-9.tgz
$ cd circos-0.69-9</code>

Circos needs some Perl modules, check which we satisfy already with our Perl 5.28.2 package:

<code>$ module load perl/5.28.2
$ ./bin/circos -modules</code>

Create directory for Perl modules and install missing modules with cpanm:

<code>
$ sudo mkdir -p /export/apps/circos/0.69-9/lib/perl5
$ sudo chown -R aorth /export/apps/circos/0.69-9
$ cpanm -l /export/apps/circos/0.69-9/ Clone Config::General Font::TTF::Font
$ sudo yum install gd-devel
$ cpanm -l /export/apps/circos/0.69-9/ GD GD::Polyline
$ sudo yum remove gd-devel
$ cpanm -l /export/apps/circos/0.69-9/ List::MoreUtils Math::Bezier Math::Round Math::VecStat
$ cpanm -l /export/apps/circos/0.69-9/ Params::Validate Readonly Regexp::Common SVG Set::IntSpanStatistics::Basic Text::Format
</code>

I don't install all the missing modules at once because sometimes they have errors and it's easier to track them down when you do less in one go.

Test again:

<code>$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5 ./circos -modules</code>

When all module requirements are satisfied continue the installation:

<code>$ cd /tmp/src/circos-0.69-9
$ cp -r * /export/apps/circos/0.69-9</code>

Add install directory to PATH and PERL5LIB and try to run it:

<code>$ export PATH=$PATH:/export/apps/circos/0.69-9/bin
$ export PERL5LIB=$PERL5LIB:/export/apps/circos/0.69-9/lib/perl5
$ circos -modules</code>

Fix permissions:

<code>$ sudo chown -R root:root /export/apps/circos/0.69-9</code>