--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Jun 01 07:20:41 2019 -0400
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable>
+    </set_environment>
+    <!--
+    Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call.
+    The intended use case was to prohibit GATK2 to collect and send data.
+    For example:
+
+    -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home
+    -->
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable>
+    </set_environment>
+
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="picard" version="1.56.0">
+        <repository changeset_revision="99a28567c3a3" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ggplot2" version="0.9.3">
+        <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>