Circleator - Installation Guide

Please note that the installation guide currently covers only installation on Linux systems, although a similar approach should also work on Windows and MAC OS X systems:

1. Install Prerequisites
   1. Install packages
   2. Install additional Perl modules
2. Download Release
3. Build and Install
4. Test

If you’re having trouble with the install process send us a message on the Circleator Google Group and we’ll try to help.

Install Prerequisites

Install packages

Install the following packages using the package manager, if you are running a variant of Linux that supports this. On Ubuntu 13.04, for example, the following packages may be installed using the Ubuntu Software Center or by running sudo apt-get install <packagename> on the command line:

• perl
• bioperl
• libbatik-java
• vcftools

Here are the corresponding web sites for these projects if it turns out that you cannot obtain them in package form, or wish to install them from source:

• Perl
• BioPerl
• Apache Batik
• VCFtools

Install additional Perl modules

Once Perl is installed the CPAN Shell can be used to install the remaining Perl dependencies, like so:

sudo cpan
install CPAN
reload cpan
install JSON
install Log::Log4perl
install SVG
install Text::CSV
install Bio::FeatureIO::gff

Note that if you do not have superuser privileges for the machine in question (i.e., to run cpan as root) then you will have to enlist the help of a superuser or install Circleator and its dependencies in your home directory or some other area to which you have write privileges.

Download Release

The most recent Circleator release can be downloaded from the Circleator releases page on GitHub. Scroll past the release notes for the version you want and click on one of the “Source code” buttons to download either a .zip or .tar.gz file.

Build and Install

Unzip or untar the downloaded file with one of the following commands:

unzip <release>.zip

or

tar xzvf <release>.tar.gz

Move into the unpacked Circleator directory:

cd <release>

To install Circleator system-wide (this requires superuser privileges):

perl Build.PL
./Build
./Build test
sudo ./Build install

To install Circleator to a different location, do this instead:

perl Build.PL --install_base=/install/path
./Build
./Build test
./Build install

Note that the tests invoked by ./Build test currently take several minutes (~5-6 depending on the speed of the machine) to run.

Test

After Circleator has been installed you can test that the installed copy is set up correctly by using the sample configuration and data files included in the distribution:

/install/path/bin/circleator --config=conf/genes-percentGC-GCskew-1.cfg --data=data/NC_011969.gbk >fig1.svg
/install/path/bin/rasterize-svg fig1.svg png

You may wish to create aliases for the circleator and rasterize-svg executables if they were not installed into a system-wide bin/ directory. Under the Bash shell, for example, the following commands can be run on the command line or placed into a ~/.bashrc file:

alias circleator="/install/path/bin/circleator"
alias rasterize-svg="/install/path/bin/rasterize-svg"