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circos-software

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:

$ wget http://circos.ca/distribution/circos-0.69-9.tgz
$ tar zxf circos-0.69-9.tgz 
$ cd circos-0.66-9

Check requirements

Circos needs some Perl modules, check which we satisfy already:

$ cd bin
$ ./circos -modules

For missing modules, check and install from the system package manager first:

$ yum install perl-Clone.x86_64 perl-Config-General.noarch perl-Font-TTF.noarch perl-Readonly.noarch perl-Regexp-Common.noarch perl-Text-Format.noarch perl-Math-Round

Install any other missing modules manually using cpanm:

  • Math::Bezier
  • Math::VecStat
  • SVG
  • Set::IntSpan

Install missing perl modules

Create directories for perl modules:

$ 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/ Math::Bezier
...

Test again

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

Continue installation

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

Try to run

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: 2020/04/07 16:36 by aorth