MUSCLE 2 Installation

The recent bundle of MUSCLE can be downloaded from the Downloads section. The bundled package contains the source code, documentation and precompiled Java archives (jar). We maintain a list of clusters where MUSCLE is already deployed.


In order to install MUSCLE from source, you need

CMake is not needed for executing MUSCLE, only for installation.

Installation of dependencies on a Debian flavored Linux


sudo apt-get install build-essential cmake ruby default-jdk

to install the minimal set of dependencies.

To resolve all features, also run

sudo apt-get install unzip subversion python-dev gfortran openmpi-bin libopenmpi-dev cmake-curses-gui

Installation of dependencies on Mac OS X

Most dependencies are installed when installing Xcode. In  Xcode 5, the command-line tools are installed by opening Preferences -> Downloads and pressing Install for "Command-line tools". Install the  Java Development Kit (JDK) from Oracle. Download CMake on  their website or use an installation manager like  HomeBrew or  MacPorts. With HomeBrew?, you can run

brew install cmake

Installation of dependencies on Scientific Linux 5.6

To install all dependencies in a single command, run

sudo yum install ruby gcc-c++ cmake jdk curl

Note: you may need to add the reference to the repository with extra packages. To do this create the file 'epel.repo' in the /etc/yum.repos.d directory. The content of the file may look as follows:

name=Extra Packages for Enterprise Linux 5 - $basearch 

Remainder of the installation

If your ruby version is 1.8.x:

ruby --version

then it is necessary to install json with the following command

sudo gem install json

When the dependencies are in place, you are ready to build and install MUSCLE. Download the muscle bundle from Downloads section, or from the command-line. Then unzip the folder, go to the build directory inside and run the command.

curl -#O
cd MUSCLE-2.1.0-sources/build

sudo ./

This installs MUSCLE in /opt/muscle. For another location, add this as the first argument to If the configuration or the libraries of the host have changed since you last built MUSCLE, run

rm CMakeCache.txt

before running the build script to forget all CMake settings.

The command

source /opt/muscle/etc/muscle.profile

should always be run before executing MUSCLE. It can help to put this command in ~/.bashrc so that it runs at login.

Finally, see if MUSCLE is working correctly:

muscle2 --version

Advanced building options

Although the script is sufficient in most cases, sometimes it can not detect where certain libraries are located, especially the libraries of the MPI example. The build settings can be modified by setting the following environment variables:

Variable Setting Example
MPI_C_COMPILER Compiler used for the C MPI example /usr/bin/mpicc
MPI_C_FLAGS Flags to give the C MPI compiler -O3 -Wall
MPI_C_INCLUDE_PATH Location of include files for C MPI /usr/include
MPI_C_LIBRARIES All libraries needed to link with for C MPI (semicolon separated) /usr/lib/;/usr/lib/

Possible build options can be evaluated by going to the build directory and running:

cmake -L ..

Even more detailed build options are found with:

cmake -LA ..

These options can be passed to cmake by setting the environment variable MUSCLE_CMAKE_OPTIONS:


For example, to build the python extension:

sudo ./

And if the Python libraries or headers cannot be found:

sudo ./

Further reading

For more information how to use MUSCLE see the Documentation and Tutorials sections.

The offered version of MUSCLE 2 in extends and improves the  package provided by Jan Hegewald, notably it has:

  • improved the installation procedure (some dependencies are already included in the bundle),
  • updated API
  • increased performance
  • decreased complexity
  • implemented a port range traversing technique for cross-cluster execution.

For MUSCLE version 1.x installation, see MUSCLE1 Installation