Installing AEGeAn

For the impatient

# Install pre-requisites with your package manager
sudo apt-get install -y build-essential git libcairo2-dev libpango1.0-dev
# Make sure /usr/local/bin is in your $PATH, and that /usr/local/lib is in
# your LD path

git clone https://github.com/genometools/genometools.git
cd genometools
make 64bit=yes
sudo make 64bit=yes install

cd ..
git clone https://github.com/standage/AEGeAn.git
cd AEGeAn
make 64bit=yes
sudo make 64bit=yes install

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, but compiling and installing does require a few prerequisites.

  • common UNIX tools for building software: specifically, GNU make and a C compiler with OpenMP support
  • GenomeTools library (see http://genometools.org/ for download and installation instructions)

While not a strict requirement, fully leveraging the graphics capabilities provided by AEGeAn requires that the system also have an installation of the Cairo graphics library (see the GenomeTools documentation).

Downloading

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 to work with a 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

It is generally assumed that the user will follow standard Linux/UNIX procedures when downloading, compiling, and installing the GenomeTools prerequisite. The default install directory is /usr/local, which means that we assume the GenomeTools binaries have been installed in /usr/local/bin and the shared libraries have been installed in /usr/local/lib.

If this is the case, then the default installation procedure should work just fine. From the directory containing the AEGeAn source code distribution, enter the following commands.

make
make install # requires root access

If you have some reason to install GenomeTools in some other directory (e.g. if you don’t have permissions to modify /usr/local), this should not be a problem for AEGeAn. You must simply tell AEGeAn where to find GenomeTools. For example, if you installed GenomeTools in /home/alice/local, then you must indicate this fact when compiling AEGeAn.

The following make options are available if you encounter any problems during installation or if you want to customize your installation.

  • 64bit=yes if you want compile for a 64-bit architecture
  • cairo=no if your system does not have Cairo graphics libraries installed (you will not be able to generate graphics)
  • GT_INSTALL_DIR=? if you did not install GenomeTools in /usr/local
  • prefix=? to install AEGeAn in a directory other than /usr/local (e.g. if you do not have admin privileges)

For example, if I need to install GenomeTools and AEGeAn in my home directory /home/alice, then I could do something like this.

test -d /home/alice/local/src || mkdir -p /home/alice/local/src

cd /home/alice/local/src
git clone https://github.com/genometools/genometools.git
cd genometools
make prefix=/home/alice/local 64bit=yes
make prefix=/home/alice/local 64bit=yes install

cd /home/alice/local/src
git clone git://github.com/standage/AEGeAn.git
cd AEGeAn
make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local
make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local install

Remember that if you install the GenomeTools library in a non-standard location, you will need to make sure that the AEGeAn binariescan find that library at runtime. This can be done on a temporary basis using the LD_LIBRARY_PATH environmental variable or on a permanent system-wide basis using the ldconfig command.

Although the /usr/local directory is the standard install location for third party libraries, on some distributions this directory is not pre-configured. If you use the default install locations and still run into problems, make sure that /usr/local/bin is in your path (using the export or setenv commands) and that /usr/local/lib is in the LD path (using the ldconfig command).

If you are not familiar with system administration, see the appendix below, which includes instructions for installing prerequisites and setting up system paths on a variety of operating systems.

Appendix: system setup

Below are instructions for installing prerequisites and configuring system paths for the most common operating systems. You’ll want to

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

    echo $PATH | grep /usr/local/bin > /dev/null
    if [ $? != 0 ]; then
      export PATH=/usr/local/bin:$PATH
      echo 'export PATH=/usr/local/bin:$PATH' >> /etc/bashrc
    fi
    grep '/usr/local/lib' /etc/ld.so.conf /etc/ld.so.conf.d/* > /dev/null
    if [ $? != 0 ]; then
      echo '/usr/local/lib' >> /etc/ld.so.conf.d/genometools-x86_64.conf
    fi
    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)

    echo $PATH | grep /usr/local/bin > /dev/null
    if [ $? != 0 ]; then
      export PATH=/usr/local/bin:$PATH
      echo 'export PATH=/usr/local/bin:$PATH' >> /etc/bashrc
    fi
    grep '/usr/local/lib' /etc/ld.so.conf /etc/ld.so.conf.d/* > /dev/null
    if [ $? != 0 ]; then
      echo '/usr/local/lib' >> /etc/ld.so.conf.d/genometools-x86_64.conf
    fi
    /sbin/ldconfig
    yum install -y git cairo-devel pango-devel
    
  • Mac OS X (tested on Mac OS 10.6)

    # Download and install Git: http://git-scm.com
    # Download and install the Fink package manager: http://www.finkproject.org/download
    # Then install the following packages using Fink
    apt-get install -y cairo-devel ncurses-devel pango1-xft2-ft219-dev
    

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