# HG changeset patch
# User bgruening
# Date 1416013125 18000
# Node ID 32fc68e671b530100ede9b7a5e950eb7f3f2341d
# Parent  934a103f88f9526f8ab9ed14bb79d1899b5e56ce
Uploaded

diff -r 934a103f88f9 -r 32fc68e671b5 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 13 18:19:55 2014 -0500
+++ b/tool_dependencies.xml	Fri Nov 14 19:58:45 2014 -0500
@@ -6,19 +6,17 @@
     <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>
+                    <!-- libxml2 needs to be sourced after R because R also was compiled against a different version of libxml2 -->
+                    <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>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_2_10/getopt_1.20.0.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>
@@ -39,7 +37,7 @@
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/RSQLite_1.0.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/sendmailR_1.2-1.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/stringr_0.6.2.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/XML_3.98-1.1.tar.gz</package>
+                    <package>http://cran.r-project.org/src/contrib/Archive/XML/XML_3.95-0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_6_1/xtable_1.7-4.tar.gz</package>
                     <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>