--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Nov 05 21:11:49 2014 -0500
@@ -0,0 +1,86 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fastx_toolkit" version="0.0.13">
+        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="0.12.7">
+        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+	<package name="R" version="3.0.1">
+	   <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="degseq" version="1.20.0">
+		<install version="1.0">
+		   <actions>
+		      <action type="set_environment_for_install">
+                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.0.1" />
+                    </repository>
+              </action>
+		      <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
+		   </actions>
+		</install>
+	</package>
+
+	<package name="threads" version="1.96">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
+			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
+			 <action type="shell_command">make</action>
+			 <action type="shell_command">make install</action>
+			 <action type="set_environment">
+			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+
+
+	<package name="Parallel-ForkManager" version="1.06">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
+			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
+			 <action type="shell_command">make</action>
+			 <action type="shell_command">make install</action>
+			 <action type="set_environment">
+			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+
+	<package name="SVG" version="2.59">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
+			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
+			 <action type="shell_command">make</action>
+			 <action type="shell_command">make install</action>
+			 <action type="set_environment">
+			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+
+	<package name="Boost-Graph" version="1.4">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/D/DB/DBURDICK/BoostGraph/Boost-Graph-1.4.tar.gz</action>
+			 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
+			 <action type="shell_command">make</action>
+			 <action type="shell_command">make install</action>
+			 <action type="set_environment">
+			   <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+
+</tool_dependency>