Configure mono for Array Suite v10.1

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Array Suite 10.1 uses the .NET 4.5 framework, which brings several improvements, but also requires an updated version of mono compared to previous installations. Benchmarking tests have identified mono4.0.4 as the best version for launching Array Server, and mono4.8.1 is best for launching all analysis jobs.

ArrayServer.cfg should be configured to use mono4.8.1, by modifying the following parameters:

HPC installations should modify clusteralign.sh and clustersummary.sh to use mono4.8.1 on all analysis nodes:

Array Server Cloud analysis works well with mono4.0.4, and the default OmicSoft AMIs include mono4.0.4 but we recommend installing mono4.8.1 on custom analysis AMIs and adding mono4.8.1 to the $PATH variable, so that mono4.8.1 will be used when Array Server calls mono without specifying an explicit path.

For example, in your Array Server analysis AMI, add the following to ~/.profile : PATH="$PATH:/usr/mono4.8.1/bin"

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