--- a/tool_dependencies.xml	Tue Mar 11 07:42:09 2014 -0400
+++ b/tool_dependencies.xml	Wed Feb 18 11:36:59 2015 -0500
@@ -15,38 +15,12 @@
     </set_environment>
 
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="9f412e12b103" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="8b98841b6b2f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="picard" version="1.56.0">
-        <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-
-    <package name="gatk2_r_dependencies" version="2.8">
-        <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-
-                    <repository changeset_revision="2c0a13200a73" name="package_r_2_11_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="R" version="2.11.0" />
-                    </repository>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/colorspace_1.2-4.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/stringr_0.6.2.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/RColorBrewer_1.0-5.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/dichromat_2.0-0.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/munsell_0.4.2.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/labeling_0.2.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/plyr_1.8.1.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/digest_0.6.4.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/gtable_0.1.2.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/reshape2_1.2.2.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/scales_0.2.3.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/proto_0.3-10.tar.gz</package>
-                        <package>https://github.com/bgruening/download_store/raw/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            R depencies for GATK2.
-        </readme>
+    <package name="ggplot2" version="0.9.3">
+        <repository changeset_revision="ade406d47752" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>