--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 03 18:38:00 2014 -0400
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="samtools" version="0.1.19">
+      <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.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>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                  <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$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="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.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
+        transcriptome assembler, although it can borrow algorithmic techniques
+        from de novo genome assembly to help with transcript assembly. Its input
+        can include not only the spliced read alignments used by reference-based
+        assemblers, but also longer contigs that were assembled de novo from
+        unambiguous, non-branching parts of a transcript.</readme>
+    </package>
+</tool_dependency>