--- a/tool_dependencies.xml	Wed May 10 09:05:49 2017 -0400
+++ b/tool_dependencies.xml	Wed May 10 11:24:30 2017 -0400
@@ -16,11 +16,6 @@
                   <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                       <package name="R" version="3.2.1" />
                     </repository>
-                    <action type="download_by_url">http://depot.galaxyproject.org/software/libx11/libx11_1.5.0_src_all.tar.bz2</action>
-        <action type="move_directory_files">
-          <source_directory> . </source_directory>
-          <destination_directory> $INSALL_DIR </destination_directory>
-            </action>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>
                     <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.1.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz</package>
@@ -125,14 +120,13 @@
                     <package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.2.4.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_2.0.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/rgl/rgl_0.95.1441.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/Archive/NMF/NMF_0.20.5.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/Archive/rstudioapi/rstudioapi_0.2.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/Archive/devtools/devtools_1.6.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/Archive/rgl/rgl_0.95.1201.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/mixOmics_6.1.2.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/bumphunter_1.10.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/minfi_1.16.1.tar.gz</package>