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-1.5.3.tar.gz tar xzf genometools-1.5.3.tar.gz cd genometools-1.5.3 make 64bit=yes sudo make 64bit=yes install # Download, compile, and install the AEGeAn Toolkit git clone https://github.com/standage/AEGeAn.git cd AEGeAn make sudo make install # Make sure that the compiler/linker can find the GenomeTools and AEGeAn # libraries sudo sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/aegean-x86_64.conf' sudo ldconfig
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).
The easiest way download the latest and greatest version of AEGeAn (including the most recent updates) is to clone from Github.
git clone https://github.com/standage/AEGeAn.git
Alternatively, you can download an archive of the source from https://github.com/standage/AEGeAn.
If you would prefer instead to work with a more thoroughly tested stable release, do one of the following.
- If you used git to clone AEGeAn, then run git tag to list all stable releases. Then before compiling run git checkout vx.y.z where vx.y.z is the latest stable release.
- Go to AEGeAn’s release page on Github and download an archive of the latest release.
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.
See the section labeled Compilation flags for a complete description of configurable settings for compilation and installation.
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 GenomeTools and AEGeAn in $DIR rather than the default directory /usr/local
- 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