# HG changeset patch
# User bgruening
# Date 1375443208 14400
# Node ID 6d4dbaa47b83935bd5bb9724186baa4ee13f6916
# Parent  adb7a2fbdbbbd3296187a5d031624181413059a0
Uploaded

diff -r adb7a2fbdbbb -r 6d4dbaa47b83 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 01 08:23:50 2013 -0400
+++ b/tool_dependencies.xml	Fri Aug 02 07:33:28 2013 -0400
@@ -1,23 +1,38 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="deseq2" version="1.0.17">
         <install version="1.0">
             <actions>
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="4dba1ce455da" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
                 </action>
 
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/BiocGenerics_0.6.0.tar.gz</action>
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/IRanges_1.18.2.tar.gz</action>
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/annotate_1.38.0.tar.gz</action>
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/GenomicRanges_1.12.4.tar.gz</action>
+<action type="download_file">http://cran.fhcrc.org/src/contrib/Rcpp_0.10.4.tar.gz</action>
+<action type="download_file">http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.3.900.0.tar.gz</action>
+<action type="download_file">http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz</action>
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/genefilter_1.42.0.tar.gz</action>
+<action type="download_file">http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz</action>
+<action type="download_file">http://bioconductor.org/packages/2.12/bioc/src/contrib/DESeq2_1.0.18.tar.gz</action>
+
+
+
                 <action type="make_directory">$INSTALL_DIR/deseq2/</action>
                 <action type="shell_command">
                     export PATH=$PATH:$R_HOME/bin &amp;&amp; 
                     export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp; 
-                    Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('DESeq2')"
+
+                    Rscript -e "install.packages(c("BiocGenerics_0.6.0.tar.gz","IRanges_1.18.2.tar.gz","annotate_1.38.0.tar.gz","GenomicRanges_1.12.4.tar.gz","Rcpp_0.10.4.tar.gz","RcppArmadillo_0.3.900.0.tar.gz","locfit_1.5-9.1.tar.gz","genefilter_1.42.0.tar.gz","RColorBrewer_1.0-5.tar.gz","DESeq2_1.0.18.tar.gz",),lib="$INSTALL_DIR/deseq2/",  repos=NULL, dependencies=FALSE)"
+
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>