--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jul 17 16:35:11 2015 -0400
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="monocle" version="1.0.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.1.2" />
+                    </repository>
+                    <package>http://cran.fhcrc.org/src/contrib/VGAM_0.9-6.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/data/experiment/src/contrib/HSMMSingleCell_1.0.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocGenerics_0.12.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/Biobase_2.26.0.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/digest_0.6.8.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/gtable_0.1.2.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/reshape2_1.4.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/dichromat_2.0-0.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/munsell_0.4.2.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/labeling_0.3.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/scales_0.2.4.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/proto_0.3-10.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/MASS_7.3-39.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/ggplot2_1.0.0.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/lattice_0.20-30.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/Matrix_1.1-5.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/igraph_0.7.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/cluster_2.0.1.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/combinat_0.0-8.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/fastICA_1.2-0.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/irlba_1.0.3.tar.gz</package>
+                    <package>http://cran.fhcrc.org/src/contrib/matrixStats_0.14.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/limma_3.22.4.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/monocle_1.0.0.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        Analysis tools for single-cell expression experiments.
+
+Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to 
+progress through a biological process, without knowing ahead of time which genes define progress through that process.
+Monocle also performs differential expression analysis, clustering, visualization, 
+and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
+
+Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS and Rinn JL (2014). “The dynamics and regulators of cell fate decisions are revealed by pseudo-temporal ordering of single cells.” Nature Biotechnology. 
+
+http://www.bioconductor.org/packages/release/bioc/html/monocle.html
+
+        </readme>
+    </package>
+</tool_dependency>