= Installation =

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

== Dependencies ==
The core functionality of the MUSCLE is written in Java. To be able to integrate native code with the MUSCLE, there is also a native part which is written in C++. Bootstrapping and platform independent configuration is done with a highly flexible setup mechanism written in Ruby. 

In order to use the MUSCLE, you need a recent Java runtime. You can obtain it at either http://www.java.com/en/download/index.jsp (Sun-Java) or http://openjdk.java.net/ (Open-JDK). 

A Ruby installation can be downloaded from: [[http://www.ruby-lang.org/en/downloads/]]. The MUSCLE does currently not work with Ruby 1.9.1 or newer. For ruby 1.8.x the json library is also required - install it with e.g. sudo gem install json.  In principle it should be possible to run MUSCLE with JRuby instead of the standard Ruby.


== General Instructions ==
If the dependencies are in place, you are ready to use the MUSCLE. No compilation required!
Extract the download, e. g.
{{{
#!div style="font-size: 90%"
{{{#!sh
$ unzip MUSCLE_2009-10-08_10-39-10.zip
}}}
}}}
Change your working directory to the the MUSCLE directory (e. g.)
{{{
#!div style="font-size: 90%"
{{{#!sh
$ cd MUSCLE_2009-10-08_10-39-10
}}}
}}}
See if the MUSCLE is working correctly
{{{
#!div style="font-size: 90%"
{{{#!sh
$ ./src/ruby/muscle.rb --version
}}}
}}}

In case you plan to use the MUSCLE with native code, you will have to compile the native library part of the MUSCLE using a C++ compiler (such as g++). The build script belonging to the MUSCLE also has a target to build the native libraries. This requires a C++ compiler and CMake (http://www.cmake.org/) to be available. You can also use
your favourite IDE/build system instead.

== What’s in the bundle? ==
The MUSCLE download bundle contains the following items:
* '''build''' - This directory contains the compiled Java bytecode and C++ libraries.
* '''build.rb'''  - The build script. It can compile the java sources, build jar archives build the native shared libraries.
* '''CMakeLists.txt''' - The configuration file for cmake. Only needed if the native libraries are to be built. This file is used by the build.rb, you do not have to call cmake manually.
* '''doc''' - The documentation files.
* '''OTF''' - The configuration and helper scripts for OTF trace logger. 
* '''src''' - This directory contains the MUSCLE source code.
* '''thirdparty''' - The MUSCLE will automatically load third-party libraries which are in this directory.

== Installation example - Scientific Linux 5.6 ==
1. Check if proper version of ruby is already installed in the system, otherwise install it:
{{{
#!div style="font-size: 90%"
{{{#!sh
ruby --version
-bash: ruby: command not found

yum install ruby
...
ruby --version
ruby 1.8.5 (2006-08-25) [x86_64-linux]
}}}
}}}

2. Check if recen Java SE Runtime Environment (JRE) or Java SE Development Kit (JDK) are present in your system. As the precompiled MUSCLE package is already included at build/muscle.jar you usually do not need to compile the Java sources and JRE is fully sufficient. If you want to recompile the Java part of the MUSCLE, a recent Java compiler is also required (javac).  
{{{
#!div style="font-size: 90%"
{{{#!sh
yum install jdk
}}}
}}}

3. Set required environment variables
{{{
#!div style="font-size: 90%"
{{{#!sh
export JAVA_HOME=/usr/java/jdk1.6.0_26
export PATH=$JAVA_HOME/bin:$PATH
}}}
}}}

4. Download the muscle bundle from [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], e.g.
{{{
#!div style="font-size: 90%"
{{{#!sh
wget http://apps.man.poznan.pl/trac/muscle/downloads/muscle-1.0.1.zip
}}}
}}}

5. Extract the package:
{{{
#!div style="font-size: 90%"
{{{#!sh
unzip muscle-1.0.1.zip
}}}
}}}

6. See if the MUSCLE is working:
{{{
#!div style="font-size: 90%"
{{{#!sh
cd muscle-1.0.1
./src/ruby/muscle.rb --version
}}}
}}}


= temp =
add epel repo to the yum.repos.d
yum install gcc
yum install cmake