Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.
What is less immediately apparent until you start digging into the documentation is that actually making Circos run is a bit of a trick. I needed it not only running, but packaged for InstaDMG and Casper distribution. The documentation links to a variety of sources that are a confusing mash of helpful, slightly outdated, now-wrong and missing. To keep myself sane, I decided to document my own process, thus this post.
Easily the best starting point is Paulo Nuin’s excellent and clearly-written install procedure. Unfortunately, even at 10 months old, it’s slipping slightly out of date, and packages available from MacPorts enable skipping a few steps. Here’s how I did things.. A general familiarity with the command line is assumed.
Gather Your Materials
Other instructions provide direct links to files. Those links go stale quickly, so I’ve linked to source directories where possible.
- Circos (currently at 0.63-4)
- GD perl module (I have elected to use 2.49 rather than the current version, for reasons I shall explain shortly)
- JAMF Composer (or packaging tool of your choice, but I highly recommend something capable of snapshot comparisons…I won’t cover packaging this manually, as the tree just becomes needlessly complex)
Set Up Your Environment
Standard packaging rules: Clean system with no other apps running. I set mine up in a Mountain Lion VM and it worked a treat.
- Install MacPorts
- Install Xcode
- Launch Xcode and accept the license agreement and device support install
- Open Preferences > Downloads and install the Command Line Tools
- Quit Xcode
- Configure and update cpan
- Open Terminal and issue the following commands (accepting the defaults as prompted)
- sudo cpan
- install CPAN <- Case sensitive
- reload cpan
Take Your Snapshot
At this point you’re ready to start installing the modules required to run Circos, so take your starting snapshot. This will be a simple, standard package.
Install and Test Circos
Decompress the Circos download, and put the resulting directory where ever you want to run Circos for simplicity’s sake, I followed Paulo’s suggestion and placed it at /Applications/circos-0.63-4/. Circos comes with its own module tester, so let’s use it. Open Terminal, and
cd /Applications/circos-0.63-4/ ./test.modules
This should return a list of installed and missing modules needed to run Circos. On a vanilla 10.8 install, that’ll look about like this:
ok Carp ok Clone fail Config::General is not usable (it or a sub-module is missing) ok Cwd ok Data::Dumper ok Digest::MD5 ok File::Basename ok File::Spec::Functions ok File::Temp ok FindBin fail Font::TTF::Font is not usable (it or a sub-module is missing) fail GD is not usable (it or a sub-module is missing) fail GD::Image is not usable (it or a sub-module is missing) fail GD::Polyline is not usable (it or a sub-module is missing) ok Getopt::Long ok IO::File ok List::MoreUtils ok List::Util fail Math::Bezier is not usable (it or a sub-module is missing) ok Math::BigFloat ok Math::Round fail Math::VecStat is not usable (it or a sub-module is missing) ok Memoize ok POSIX ok Params::Validate ok Pod::Usage fail Readonly is not usable (it or a sub-module is missing) ok Regexp::Common fail Set::IntSpan is not usable (it or a sub-module is missing) ok Storable ok Sys::Hostname ok Text::Balanced fail Text::Format is not usable (it or a sub-module is missing) ok Time::HiRes
Install items required by Circos
It’s those “fail” entries we’re concerned with, of course. So at a bare minimum, we need to install:
Config::General Font::TTF::Font GD GD::Image GD::Polyline Math::Bezier Math::VecStat Readonly Set::IntSpan Text::Format
We’ll do this using a mix of CPAN, build from source, and MacPorts. Since GD2 is available via MacPorts, let’s start there. The trick to know is that as of the 2.0.35 build of GD2, letting MacPorts install the fontconfig dependency seems to hard-hang the process. So:
sudo port install fontconfig sudo port install gd2
Now, crank up CPAN, and let’s get started on the perl modules. Note that CPAN commands are case sensitive.
sudo cpan install Config::General install Font::TTF::Font install Math::Bezier install Math::VecStat install Readonly install Set::IntSpan install Text::Format exit
If you run the test.module script at this point, everything should pass but the GD modules. Let’s take care of that. (A word about versions: There is a newer version of GD available from the BitBucket repo Paulo mentions, but they’ve changed compilation methods and I can’t for the life of me get it to build. If you can, I’d appreciate a how-to!) In the Finder, locate your GD-2.49 download and decompress it. In Terminal, move to the GD-2.49 directory you just decompressed, and issue the following commands:
perl Makefile.PL make sudo make install
When that’s done, cd back to Circos’ bin directory and re-run test.modules. Everything should now register okay. Then:
sudo ln -s /usr/bin/env /bin/env
This symlinks env to /bin. Circos is picky about finding it there. You could also add it to your path. At this point, Circos should be ready to rock.
cd /Applications/circos-0.63-4/example ./run ls -lah
You should see circos.png and circos.svg with a creation date/time of…well, now.
Take your finished snapshot
All that remains is to finish your snapshot and package Circos! Use your standard procedure…no tweaking of permissions is required. But be sure to remove the extraneous junk that CPAN, et. al. leave strewn around your home directory!