Installing AEGeAn

For the impatient

# Install pre-requisite packages with your OS's package manager
sudo apt-get install -y build-essential git libcairo2-dev libpango1.0-dev

# Download, compile, and install the GenomeTools package
curl -O http://genometools.org/pub/genometools-1.5.9.tar.gz
tar xzf genometools-1.5.9.tar.gz
cd genometools-1.5.9
make
sudo make install
cd ..

# Make sure that the compiler/linker can find the GenomeTools library
sudo sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/genometools-x86_64.conf'
sudo ldconfig

# Download, compile, and install the  AEGeAn Toolkit
curl https://github.com/standage/AEGeAn/archive/vx.y.z.tar.gz > AEGeAn-x.y.z.tar.gz
tar xzf AEGeAn-x.y.z.tar.gz
cd AEGeAn-x.y.z
make test
sudo make install install-scripts
sudo ldconfig # Update linker config again

Prerequisites

In principle, AEGeAn should compile and run on any POSIX-compliant UNIX system (Linux, Mac OS X, Cygwin), although in practice, it has only been tested on Linux and Mac systems. Native Windows support is not anticipated any time soon.

We have made an effort to minimize dependency on external software. Aside from the GenomeTools library (which is included in the AEGeAn source code distribution), compiling and installing AEGeAn requires only GNU make and a C compiler.

While not a strict requirement, fully leveraging the graphics capabilities provided by AEGeAn (through GenomeTools) requires that the system also have an installation of the Cairo graphics library (see “Appendix: system setup” for platform-specific installation instructions).

Downloading

Official stable releases of the AEGeAn Toolkit can be downloaded from the Releases tab on the AEGeAn GitHub page. Alternatively, you can always download the latest and greatest version of AEGeAn (most recently updates, though not guaranteed to be stable) by cloning the Git repository.

git clone https://github.com/standage/AEGeAn.git

Note: AEGeAn uses Semantic Versioning for labeling stable releases.

Compiling and installing

The instructions under the section labeled “For the impatient” are a good starting point for most users. Chances are many users will be able to successfully install by running those commands verbatim. The first few commands are specific to Debian-based Linux operating systems such as Ubuntu. If you are using a different operating system, please see “Appendix: system setup” for platform-specific instructions. After running those commands, complete the installation by running make and make install.

The AEGeAn Toolkit includes several ancillary scripts for processing annotation data. To install these along with the C programs, invoke the make install-scripts command.

See the section labeled Compilation flags for a complete description of configurable settings for compilation and installation.

Compilation flags

Compilation settings can be configured using the following flags with the make command.

  • 64bit=no: do not compile for a 64-bit architecture
  • cairo=no: compile without graphics support (if your system does not have the Cairo graphics libraries installed)
  • prefix=$DIR: install AEGeAn in $DIR rather than the default directory /usr/local; it is expected that GenomeTools is installed with the same prefix
  • optimize=yes: enable performance optimization for the AEGeAn code
  • errorcheck=no: allow code to compile even if there are warnings
  • debug=no: disable debugging support
  • clean: remove all compiler-generated files

For example, if you want to compile the code with performance optimizations enabled and graphics support disabled, run make optimize=yes cairo=no instead of just make.

Compiling without administrative privileges

The default installation location is /usr/local/, which means:

  • programs are installed in /usr/local/bin
  • header files are installed in /usr/local/include
  • libraries are installed in /usr/local/lib
  • auxiliary data files are installed in /usr/local/share

If you do not have administrative privileges on your machine, then you will not be able to run make install without specifying an alternative installation directory with prefix. Creating an installation directory within your home directory, as shown in the following example, is recommended.

mkdir ~/local
make prefix=~/local
make prefix=~/local install

This will install the programs in ~/local/bin, the libraries in ~/local/lib, etc. You will probably want to add ~/local/bin to your PATH environmental variable and ~/local/lib to your LD_LIBRARY_PATH environmental variable (or DYLD_LIBRARY_PATH on Mac OS X).

Appendix: system setup

Below are instructions for installing prerequisites and configuring system paths for the most common operating systems. Note that running these commands requires administrative/sudo privileges.

  • Debian-based systems including Ubuntu, Mint/LMDE, etc (tested on Ubuntu 11.10)

    sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/aegean-x86_64.conf'
ldconfig
apt-get install -y build-essential git libcairo2-dev libpango1.0-dev

  • Red Hat-based systems including CentOS, Fedora, etc (tested on CentOS 5.3)

    sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/aegean-x86_64.conf'
/sbin/ldconfig
yum install -y git cairo-devel pango-devel

  • Mac OS X

    # Install Homebrew: http://brew.sh/
# Then use the brew command to install GenomeTools
brew install genometools