# HG changeset patch
# User bgruening
# Date 1380871077 14400
# Node ID ce304c51f69b5d2216e6fb215ece64d1943dd9d4
# Parent  d3b111f922a3c97b752148cdad033d7f84529b1f
Uploaded

diff -r d3b111f922a3 -r ce304c51f69b tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 01 10:47:25 2013 -0400
+++ b/tool_dependencies.xml	Fri Oct 04 03:17:57 2013 -0400
@@ -6,7 +6,7 @@
                 <!-- 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">
+                    <action type="move_file" rename_to="muscle">
                         <source>../muscle3.8.31_i86darwin64</source>
                         <destination>$INSTALL_DIR/muscle</destination>
                     </action>
@@ -14,31 +14,34 @@
                 <!-- Download the binaries for MUSCLE compatible with 32-bit OSX. -->
                 <actions os="darwin" architecture="i386">
                     <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86darwin32.tar.gz</action>
-                    <action type="move_file">
-                        <source>../muscle3.8.31_i86darwin32</source>
-                        <destination>$INSTALL_DIR/muscle</destination>
+                    <action type="move_file" rename_to="muscle">
+                        <source>muscle3.8.31_i86darwin32</source>
+                        <destination>$INSTALL_DIR</destination>
                     </action>
                 </actions>
                 <!-- Download the binaries for MUSCLE compatible with 64-bit Linux. -->
                 <actions os="linux" architecture="x86_64">
                     <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz</action>
-                    <action type="move_file">
-                        <source>../muscle3.8.31_i86linux64</source>
-                        <destination>$INSTALL_DIR/muscle</destination>
+                    <action type="move_file" rename_to="muscle">
+                        <source>muscle3.8.31_i86linux64</source>
+                        <destination>$INSTALL_DIR</destination>
                     </action>
                 </actions>
                 <!-- Download the binaries for MUSCLE compatible with 32-bit Linux. -->
                 <actions os="linux" architecture="i386">
                     <action type="download_by_url">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz</action>
-                    <action type="move_file">
-                        <source>../muscle3.8.31_i86linux32</source>
-                        <destination>$INSTALL_DIR/muscle</destination>
+                    <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">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
-                    <action type="shell_command">cd src &amp;&amp; make</action>
+                    <action type="shell_command">ls -l &gt; $INSTALL_DIR/foo.txt</action>
+                    <action type="shell_command">ls -l > $INSTALL_DIR/foo.txt</action>
+                   <action type="shell_command">make</action>
+
                     <action type="move_file">
                         <source>muscle</source>
                         <destination>$INSTALL_DIR</destination>