--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 30 11:51:55 2013 -0400
@@ -0,0 +1,67 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+    <package name="muscle" version="3.8.31">
+        <install version="1.0">
+            <actions_group>
+                <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86darwin64.tar.gz</action>
+                    <action type="move_file" rename_to="muscle">
+                        <source>../muscle3.8.31_i86darwin64</source>
+                        <destination>$INSTALL_DIR/muscle</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for MUSCLE compatible with 32-bit OSX. -->
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86darwin32.tar.gz</action>
+                    <action type="move_file" rename_to="muscle">
+                        <source>muscle3.8.31_i86darwin32</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for MUSCLE compatible with 64-bit Linux. -->
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz</action>
+                    <action type="move_file" rename_to="muscle">
+                        <source>muscle3.8.31_i86linux64</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for MUSCLE compatible with 32-bit Linux. -->
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz</action>
+                    <action type="move_file" rename_to="muscle">
+                        <source>muscle3.8.31_i86linux32</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
+                <actions>
+                    <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
+                    <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
+                    <action type="shell_command">sed -i 's/-static//g' src/mk</action>
+                    <action type="shell_command">make -C src/</action>
+                    <action type="move_file">
+                        <source>src/muscle</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X MUSCLE
+binaries, which is faster than performing a local compilation,
+avoids any issues with build dependencies, and is more reproducible between
+installations as there is no variability from the compiler or library 
+versions.
+If the download attempt fails, compiling MUSCLE from source is attempted.
+
+For more details, see:
+http://www.drive5.com/muscle/manual/
+        </readme>
+    </package>
+</tool_dependency>