<commit_before>Installing AEGeAn
=================


For the impatient
-----------------

.. code-block:: bash

    # 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
    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/v0.11.0.tar.gz > AEGeAn-0.11.0.tar.gz
    tar xzf AEGeAn-0.11.0.tar.gz
    cd AEGeAn-0.11.0
    make test
    sudo make install
    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 <https://github.com/standage/AEGeAn/releases>`_ 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.<commit_msg>Fixed docs [skip ci]<commit_after>Installing AEGeAn
=================


For the impatient
-----------------

.. code-block:: bash

    # 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-1.5.4.tar.gz
    tar xzf genometools-1.5.4.tar.gz
    cd genometools-1.5.4
    make 64bit=yes
    sudo make 64bit=yes 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/v0.12.0.tar.gz > AEGeAn-0.12.0.tar.gz
    tar xzf AEGeAn-0.12.0.tar.gz
    cd AEGeAn-0.12.0
    make test
    sudo make install
    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 <https://github.com/standage/AEGeAn/releases>`_ 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.
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