Install Mono 4.0.4

Download Mono 4.0.4

wget -c http://download.mono-project.com/sources/mono/mono-4.0.4.1.tar.bz2

The bz2 file can be saved to a temporary location, e.g. ~/temp/

Compile and install

On the command line, type

tar jxvf mono-4.0.4.1.tar.bz2
cd  mono-4.0.4
./configure  --prefix=/opt/mono-4.0.4 --with-large-heap=yes
make
make  install

Note:

   The location of mono installed is set by the option "--prefix" in the configure step, which can be changed to another location.
   The option --with-large-heap=yes is to enable support for GC heaps larger than 3gb, which is required for NGS alignment, as well as some Array Server functions) 

Double check mono installation and version

ls /opt/mono-4.0.4/bin/mono* -all
/opt/mono-4.0.4/bin/mono --version
/opt/mono-4.0.4/bin/mono-sgen --version

Install Mono 4.8.1

If not done already, install cmake.

sudo apt-get install cmake

Download Mono 4.8.1

wget -c http://download.mono-project.com/sources/mono/mono-4.8.1.0.tar.bz2

The bz2 file can be saved to a temporary location, e.g. ~/temp/

Compile and install. On the command line, type

tar jxvf mono-4.8.1.0.tar.bz2
cd  mono-4.8.1
./configure  --prefix=/opt/mono-4.8.1 --with-large-heap=yes
make
make  install

Note:

   The location of mono installed is set by the option "--prefix" in the configure step, which can be changed to another location.
   The option --with-large-heap=yes is to enable support for GC heaps larger than 3gb, which is required for NGS alignment, as well as some Array Server functions) 

Double check mono installation and version

ls /opt/mono-4.8.1/bin/mono* -all
/opt/mono-4.8.1/bin/mono --version
/opt/mono-4.8.1/bin/mono-sgen --version

Libgdiplus

The mono libgdiplus package must be installed (either using yum, apt-get, or installing from source at libgdiplus). In addition, the mono config file must be edited to explicitly specify the location of libgdiplus.so.

cd /opt
wget http://download.mono-project.com/sources/libgdiplus/libgdiplus-2.10.tar.bz2
tar  jxvf   libgdiplus-2.10.tar.bz2
cd  /opt/libgdiplus-2.10
./configure  --prefix=/opt/libgdiplus-2.10
make
make install

If installing from source, you may need to add the "/libgdiplusPrefix/lib" to the shared library search paths, and check to make sure libgdiplus library is on the shared library search paths. To check, type

$ ldconfig -p | grep libgdiplus
    libgdiplus.so (libc6,x86-64) => /opt/libgdiplus-2.10/lib/libgdiplus.so

Here the libgdiplus is installed at "/opt/libgdiplus" and has been set correctly. If not, one way to add it to the shared library path is by doing this (with root privilege),

echo "/opt/libgdiplus/lib" > /etc/ld.so.conf.d/libgdiplus.conf
ldconfig

If installing from yum, it may be necessary to additionally install the following:

yum install libgdiplus
yum install libungif libungif-devel

Edit mono config to point to libgdiplus

To connect mono and libgdiplus, modify the following config file: /MonoPrefix/etc/mono/config: Add the following line at the end of the file before </configuration>

<dllmap dll="gdiplus.dll" target="/opt/libgdiplus-2.10/lib/libgdiplus.so"/>

Further details can be found here, including a description of the error message if this is improperly performed.

Troubleshooting Libgdiplus errors

Libgdiplus compile errors