--- a/readme.rst	Mon Aug 25 17:44:53 2014 -0400
+++ b/readme.rst	Mon Jun 04 05:38:15 2018 -0400
@@ -52,14 +52,23 @@
 http://www.broadinstitute.org/gatk/guide/article?id=1250
 
 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file:
+::
+    <tool_dependency_dir>/gatk2/default/env.sh
 
-<tool_dependency_dir>/gatk2/default/env.sh
+Note that due to the manual nature of the GATK2 installation you will be getting the 
+following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph):
+::
+    Failed to resolve dependency on 'gatk2', ignoring.
+
+This is because the 
+::
+    <requirement type="package">gatk2</requirement>
+is specified but never resolved in the tool_dependencies.xml. It is safe to ignore.
 
 Finally, you should fill in additional information about your genomes and 
 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. 
 You can find them in the tool-data/ Galaxy directory.
 
-
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