= MUSCLE 2 Installation =

The recent bundle of MUSCLE can be downloaded from the [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]]. The bundled package contains the source code, documentation and precompiled Java archives (jar). We maintain a [[Clusters|list of clusters]] where MUSCLE is already deployed.

== Dependencies ==

In order to use the MUSCLE, you need

* a recent Java runtime, either [[http://www.java.com/en/download/index.jsp|Oracle-Java]] or [[http://openjdk.java.net/|Open-JDK]].
* [[http://www.ruby-lang.org/|Ruby]]
* The [[http://www.cmake.org/|CMake]] build system.

For the MUSCLE Transport Overlay, to communicate between different clusters,
* [[http://www.boost.org/|Boost]].

=== Installation of dependencies on a Debian flavored Linux ===

Run
{{{
sudo apt-get install build-essential cmake ruby libboost-dev
}}}

to install all dependencies at once.

=== 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:
{{{
[epel]
name=Extra Packages for Enterprise Linux 5 - $basearch 
 
#baseurl=http://download.fedoraproject.org/pub/epel/5/$basearch
mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=epel-5&arch=$basearch
failovermethod=priority
enabled=1
gpgcheck=0
}}}

=== Installation of dependencies on Mac OS X ===

Most dependencies are installed when installing Xcode. In [[http://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12|Xcode 4]], the command-line tools are installed by opening Preferences -> Downloads and pressing Install for "Command-line tools". For Boost and CMake, download the packages on their website or use an installation manager like [[http://mxcl.github.com/homebrew/|HomeBrew]] or [[http://www.macports.org/|MacPorts]]. With HomeBrew, you can run
{{{
brew install boost cmake
}}}

=== 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 [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], or from the command-line. Then unzip the folder, go to the build directory inside and run the {{{build.sh}}} command.
{{{
curl -#O http://apps.man.poznan.pl/trac/muscle/downloads/MUSCLE-2.0.0rc2-sources.zip
unzip MUSCLE-2.0.0rc2-sources.zip
cd MUSCLE-2.0.0rc2-sources/build

sudo ./build.sh
}}}

This installs MUSCLE in /opt/muscle. For another location, add this as the first argument to {{{build.sh}}}.

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
}}}
== 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 [[http://muscle.berlios.de/|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]]