Installation
If you experience problems during installation, please refer to the following resources before contacting me. The answers are out there and you're likely to find them much faster than I can respond to your query.
- Strawberry Perl Support (Windows)
- Installing GD with Strawberry Perl (Windows)
- Installing Perl Modules
And don't forget to open your googles!
UNIX vs Windows
If you are a Windows users, read how how Circos differes on UNIX and Windows.
Perl
For a more detailed set of instructions, see the Installation Tutorial
Linux, *NIX, Mac OS X
First, check if you have perl. You probably do. At the terminal,
> which perl /usr/bin/perl
If you see this, you have perl. On the other hand, if 'which' does not return anything
> which perl >
you don't have Perl, or the Perl binary is not in your path (which is not likely).
I won't go into the details of installing perl - there are too many ways to do it. Chances are a package (bundle, or whatever your operating system calls precompiled distributions) is available. Check at www.perl.org.
Unless you have an excellent reason, you don't want to compile your own Perl from the source code. There is nothing to be gained.
Windows
I suggest Strawberry Perl. If it's good enough for Larry, it's good enough for you.
Installing on Windows should be relatively painless.
Perl Modules
Perl comes with a large number of workhorse modules. In addition, a few other modules are required to run Circos (see requirements). All these modules are available from CPAN, the Comprehensive Perl Archive Network.
If you attempt to run Circos without having a required module, you'll see an error like this
Can't locate Missing/Module.pm in @INC (@INC contains: /home/martink/perl/5.10.0/lib/5.10.0/x86_64-linux /home/martink/perl/5.10.0/lib/5.10.0 /home/martink/perl/5.10.0/lib/site_perl/5.10.0/x86_64-linux /home/martink/perl/5.10.0/lib/site_perl/5.10.0 .). BEGIN failed--compilation aborted.
This error tells you Missing::Module is missing. Note that the module name uses :: to encode the directory of the module file. For example, if an error indicates that Set/IntSpan.pm is missing, the corresponding module name is Set::IntSpan.
Linux, *NIX, Mac OS X
To install the missing module, use the perl CPAN shell. At the terminal,
> perl -MCPAN -e shell ... cpan[1]> install Missing::Module ... ... lengthy output here, should end with a message like ... ... /usr/bin/make install -- OK ... cpan[2]> exit >
If you attempt to install a module you already have an up-to-date version for CPAN will duly inform you.
cpan[1]> install Already::Installed::Module Already::Installed::Module is up to date (1.00)
Except for GD, installing the modules should cause you no problems.
On Mac OS X you will need to install the XCode tools (which, among others, provide 'make') in order to compile modules like GD. These tools are available on the Mac OS X distribution DVD as an extra installation package.
Windows
Your Perl distribution comes with a package manager. Use it to install modules.
GD
Installing GD can be tricky, since it depends on your system's C libgd library, among others. Getting all the dependency ducks in a row ranges across the full scale of pain, from "wow that was fast" to "omg omg we're all going to die".
Many problems can arise when compiling perl's GD module. Any problem you encounter has likely been solved by others, so here's where a good Google will help.
You should compile GD with TrueType font (TTF) support (requires freetype library) as well as PNG support. It's a good idea to also include JPEG, although this software does not use that output format.
If you are not seeing any text in your output images, but expect to, this is invariably due to lack of TTF support in your GD compilation. You'll need to reinstall the module, making sure that TTF support is activated.
Circos
Because Perl is interpreted, you don't need to compile anything. That should make you happy.
To install Circos, the only thing you need to do is unpack the archive, which you've downloaded.
Linux, *NIX, Mac OS X
> tar xvfz circos-0.55.tgz ...watch files unpack... > cd circos-0.52
Windows
Use WinZip, WinRAR or whatever your favourite archive manager may be.