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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

Installation

Notes from the sysadmin during installation:

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

Check requirements

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

$ cd bin
$ ./test.modules

For missing modules, check and install from 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

Install other modules manually:

Math::Round
Math::VecStat

Install missing perl modules

Create directories for perl modules:

$ sudo mkdir -p /export/apps/circos/0.66/{share,lib,lib64}/perl5
$ sudo chown -R aorth /export/apps/circos/0.66

Prepare CPAN for installing into our prefix:

$ perl -e shell -MCPAN
cpan[1]> o conf makepl_arg "INSTALLDIRS=site PREFIX=/export/apps/circos/0.66"
cpan[2]> o conf mbuildpl_arg "--prefix /export/apps/circos/0.66"
cpan[3]> o conf commit

Then install the missing modules one by one, ie:

install Math::Round

Test again

$ PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 ./list.modules

Working!

Continue installation

$ cd ~/src/circos-0.66
$ cp -r * /export/apps/circos/0.66

Try to run

Add install dir to PATH and PERL5LIBS and try to run it:

$ PATH=$PATH:/export/apps/circos/0.66/bin $ PERL5LIB=$PERL5LIB:/export/apps/circos/0.66/lib64/perl5:/export/apps/circos/0.66/share/perl5 circos

It might complain about more missing modules, so install them also (with CPAN like above):

Math::Bezier
Set::IntSpan

Fix permissions

$ sudo chown -R root:root /export/apps/circos/0.66
circos-software.txt · Last modified: 2015/08/20 15:52 by joguya