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circos-software

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Circos

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

Information

Usage

See versions of circos which are available:

$ module avail circos

Load one version into your environment and run it:

$ module load circos/0.69-9
$ circos

Installation

Notes from the sysadmin during installation:

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

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

$ module load perl/5.28.2
$ ./bin/circos -modules

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

$ 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

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:

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

When all module requirements are satisfied continue the installation:

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

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

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

Fix permissions:

$ sudo chown -R root:root /export/apps/circos/0.69-9
circos-software.txt · Last modified: 2020/09/18 10:14 by aorth