# HG changeset patch
# User shian_su <registertonysu@gmail.com>
# Date 1416461882 -39600
# Node ID 0eb483fe920def0de5706e562a56581d68eee5f0
# Parent  fb9d6ec3223b8601aa3af8dea11ab6b10fd99afd
Uploaded

diff -r fb9d6ec3223b -r 0eb483fe920d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 20 16:06:48 2014 +1100
+++ b/tool_dependencies.xml	Thu Nov 20 16:38:02 2014 +1100
@@ -1,38 +1,32 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.1.0">
-        <repository changeset_revision="6b40f2744cde" name="package_r_3_1_0" owner="iuc" prior_installation_required="True" />
+        <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="shrnaseq" version="1.2.1">
         <install version="1.0">
             <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="6b40f2744cde" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                <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>
-                </action>
-                <action type="download_file">https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</action>
-                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/locfit_1.5-9.1.tar.gz</action>
-                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/statmod_1.4.20.tar.gz</action>
-                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/limma_3.22.1.tar.gz</action>
-                <action type="download_file">https://github.com/Shians/diffexp/raw/master/dependencies/edgeR_3.8.3.tar.gz</action>
-                
-                <action type="make_directory">$INSTALL_DIR/shrnaseq/</action>
-                <action type="shell_command">
-                    export PATH=$PATH:$R_HOME/bin &amp;&amp;
-                    export R_LIBS=$INSTALL_DIR/shrnaseq/ &amp;&amp;
-                    Rscript -e "install.packages(c('locfit_1.5-9.1.tar.gz', 'statmod_1.4.20.tar.gz', 'limma_3.22.1.tar.gz', 'edgeR_3.8.3.tar.gz'),lib='$INSTALL_DIR/shrnaseq/', repos=NULL, dependencies=FALSE)"
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/shrnaseq/</environment_variable>
+                    <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_6_1/BiocGenerics_0.12.1.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>
+                    <!-- wrapper dependency -->
+                    <package>http://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.14.tar.gz</package>
                 </action>
             </actions>
         </install>
         <readme>
-            shrnaseq analysis using edgeR bioConductor package.
-            http://bioconductor.org/packages/release/bioc/html/edgeR.html
+        Differential gene expression analysis based on the negative binomial distribution.
+        http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
         </readme>
     </package>
-
 </tool_dependency>