--- a/tool_dependencies.xml	Tue Jun 23 12:10:15 2015 -0400
+++ b/tool_dependencies.xml	Thu Dec 31 13:58:43 2015 -0500
@@ -1,21 +1,27 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="jbrowse" version="1.11.6">
-    <repository changeset_revision="d5ab749c9e97" name="package_jbrowse_1_11_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="jbrowse" version="1.12.0">
+    <repository changeset_revision="22be3ae5599d" name="package_jbrowse_1_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="bundle_jbrowse" version="1.12.0">
+    <repository changeset_revision="52153ec17769" name="package_perl_bundle_jbrowse_1_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="python" version="2.7">
-    <repository changeset_revision="44bb4258922f" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="biopython" version="1.66">
+    <repository changeset_revision="8433ee4531ff" name="package_biopython_1_66" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="perl" version="5.18">
-    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="bcbiogff" version="0.6.2">
+    <repository changeset_revision="b584674413b1" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="perl" version="5.18.1">
+    <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="samtools" version="1.2">
-    <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="bundle_jbrowse" version="1.0">
-    <repository changeset_revision="361f7cf7a442" name="package_perl_bundle_jbrowse_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="pyyaml" version="3.11">
-    <repository changeset_revision="195682051d7c" name="package_python_2_7_pyyaml_3_11" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="99267d131c05" name="package_python_2_7_pyyaml_3_11" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>