--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 30 07:34:04 2013 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="muscle" version="3.8.31">
+    <install version="1.0">
+      <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>$INSTALL_DIR/bin</destination>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
+Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
+    </readme>
+  </package>
+</tool_dependency>