# HG changeset patch
# User iuc
# Date 1424277386 18000
# Node ID 0627e8e308732cb9186611a6e1a3daebb5b09f07
# Parent  09b1ece7f3e9904727fc202a5c109aaeb35040a0
Uploaded

diff -r 09b1ece7f3e9 -r 0627e8e30873 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 01 19:08:38 2014 -0400
+++ b/tool_dependencies.xml	Wed Feb 18 11:36:26 2015 -0500
@@ -1,44 +1,44 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="samtools" version="0.1.19">
-      <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="stringtie" version="0.97">
-      <install version="1.0">
-          <actions_group>
-              <actions architecture="x86_64" os="linux">
-                  <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+	                <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
                     <action type="move_file">
-                      <source>stringtie</source>
+                        <source>stringtie</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
-                  <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
+	                <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
                     <action type="move_file">
-                      <source>stringtie</source>
+                        <source>stringtie</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                 </actions>
-                <actions>
-                  <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
-                    <action type="set_environment_for_install">
-                      <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                          <package name="samtools" version="0.1.19" />
-                        </repository>
-                    </action>
-                    <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
-                    <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
-                    <action type="shell_command">make</action>
-                    <action type="move_file">
-                      <source>stringtie</source>
-                        <destination>$INSTALL_DIR/bin</destination>
-                    </action>
-                </actions>
-                <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
+	            <actions>
+                    <package name="samtools" version="0.1.19">
+                        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+	                <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
+	                <action type="set_environment_for_install">
+	                    <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu">
+	                        <package name="samtools" version="0.1.19" />
+	                    </repository>
+	                </action>
+	                <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
+	                <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
+	                <action type="shell_command">make</action>
+	                <action type="move_file">
+	                    <source>stringtie</source>
+	                    <destination>$INSTALL_DIR/bin</destination>
+	                </action>
+	            </actions>
+	            <action type="set_environment">
+	                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+	            </action>
+	        </actions_group>
         </install>
         <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
         alignments into potential transcripts. It is primarily a genome-guided