--- a/tool_dependencies.xml	Tue Jan 27 09:01:30 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 04 13:19:09 2015 -0500
@@ -1,41 +1,41 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="squid" version="1.9g">
-      <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="squid" version="1.9g">
+        <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="randfold" version="2.0">
-      <install version="1.0">
-          <actions>
-              <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz</action>
                 <action type="set_environment_for_install">
-                  <repository changeset_revision="c1b72442ee05" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                      <package name="squid" version="1.9g" />
+                    <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="squid" version="1.9g" />
                     </repository>
                 </action>
                 <action type="shell_command">make</action>
                 <action type="move_file">
-                  <source>randfold</source>
+                    <source>randfold</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>
 
-RANDFOLD - A randsomization test for sequence secondary structure 
+RANDFOLD - A randsomization test for sequence secondary structure
 Copyright (C) 2005 Eric Bonnet - Bioinformatics &amp;amp; Evolutionary Genomics - VIB
 -----------------------------------------------------------------------------
 
-This is RANDFOLD version 2. The software compute the probability that, for a 
-given sequence, the Minimum Free Energy (MFE) of the secondary structure is 
-different from MFE computed with random sequences. 
+This is RANDFOLD version 2. The software compute the probability that, for a
+given sequence, the Minimum Free Energy (MFE) of the secondary structure is
+different from MFE computed with random sequences.
 
 For more information, see the paper published in Bioinformatics:
 
 Bonnet E, Wuyts J, Rouze P, Van de Peer Y.
-Evidence that microRNA precursors, unlike other non-coding RNAs, have lower 
+Evidence that microRNA precursors, unlike other non-coding RNAs, have lower
 folding free energies than random sequences.
 Bioinformatics. 2004 Nov 22;20(17):2911-7.
 PMID: 15217813