# HG changeset patch
# User iuc
# Date 1415920795 18000
# Node ID 934a103f88f9526f8ab9ed14bb79d1899b5e56ce
# Parent  128fe9c0477e3a218a5eaca7567ec545fb906cf1
Uploaded

diff -r 128fe9c0477e -r 934a103f88f9 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 13 13:38:21 2014 -0500
+++ b/tool_dependencies.xml	Thu Nov 13 18:19:55 2014 -0500
@@ -3,21 +3,30 @@
     <package name="R" version="3.1.0">
         <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="libxml2" version="2.9.1">
+        <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
     <package name="deseq2" version="1.6.1">
         <install version="1.0">
             <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                </action>
                 <action type="setup_r_environment">
-
                     <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="R" version="3.1.0" />
                     </repository>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/getopt_1.20.0.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/BiocGenerics_0.8.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.12.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/Rcpp_0.11.3.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/RcppArmadillo_0.4.500.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/S4Vectors_0.4.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/IRanges_2.0.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/XVector_0.6.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/GenomeInfoDb_1.2.2.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/GenomicRanges_1.18.1.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/base64enc_0.1-2.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/colorspace_1.2-4.tar.gz</package>
@@ -35,7 +44,6 @@
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/dichromat_2.0-0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/munsell_0.4.2.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/labeling_0.3.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/GenomeInfoDb_1.2.2.tar.gz</package>
 
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/foreach_1.4.2.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/digest_0.6.4.tar.gz</package>