--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 08 16:51:06 2015 -0400
@@ -0,0 +1,129 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="cairo" version="1.14.2">
+        <repository changeset_revision="59eb331c1118" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="tiff" version="4.0.3">
+        <repository changeset_revision="1720cc7e1949" name="package_tiff_4_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="freetype" version="2.5.2">
+        <repository changeset_revision="289d7796a1f1" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pixman" version="0.32.6">
+        <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libpng" version="1.6.7">
+      <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libxml2" version="2.9.1">
+        <repository changeset_revision="e5475acebd6e" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libcurl" version="7.35">
+        <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="dexseq" version="1.14">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.2.1" />
+                    </repository>
+                    <repository changeset_revision="1720cc7e1949" name="package_tiff_4_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="tiff" version="4.0.3" />
+                    </repository>
+                    <repository changeset_revision="59eb331c1118" name="package_cairo_1_14_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="cairo" version="1.14.2" />
+                    </repository>
+                    <repository changeset_revision="289d7796a1f1" name="package_freetype_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="freetype" version="2.5.2" />
+                    </repository>
+                    <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="pixman" version="0.32.6" />
+                    </repository>
+                    <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.6.7" />
+                    </repository>
+                    <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libcurl" version="7.35" />
+                    </repository>
+                    <!-- libxml2 needs to be sourced after R because R also was compiled against a different version of libxml2 -->
+                    <repository changeset_revision="e5475acebd6e" name="package_libxml2_2_9_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libxml2" version="2.9.1" />
+                    </repository>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Cairo_1.5-8.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/rjson_0.2.15.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/getopt_1.20.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/lambda.r_1.1.7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.options_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.logger_1.4.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/snow_0.3-13.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/BiocParallel_1.2.20.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/BiocGenerics_0.14.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Biobase_2.28.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/S4Vectors_0.6.4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/IRanges_2.2.7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/GenomeInfoDb_1.4.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/XVector_0.8.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/GenomicRanges_1.20.5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Rcpp_0.12.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/RcppArmadillo_0.5.400.2.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DBI_0.3.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/RSQLite_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/AnnotationDbi_1.30.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/XML_3.98-1.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/xtable_1.7-4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/annotate_1.46.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/survival_2.38-3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/genefilter_1.50.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/lattice_0.20-33.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/geneplotter_1.46.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/plyr_1.8.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/digest_0.6.8.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/gtable_0.1.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/stringi_0.5-5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/magrittr_1.5.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/stringr_1.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/reshape2_1.4.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/dichromat_2.0-0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/colorspace_1.2-6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/munsell_0.4.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/labeling_0.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/scales_0.3.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/proto_0.3-10.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/MASS_7.3-44.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/ggplot2_1.0.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Formula_1.2-1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/latticeExtra_0.6-26.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/cluster_2.0.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/rpart_4.1-10.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/nnet_7.3-11.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/acepack_1.3-3.3.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/foreign_0.8-66.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/gridExtra_2.0.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Hmisc_3.16-0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DESeq2_1.8.1.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/bitops_1.0-6.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/RCurl_1.95-4.7.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/biomaRt_2.24.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/hwriter_1.3.2.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/zlibbioc_1.14.0.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Biostrings_2.36.4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/Rsamtools_1.20.4.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/statmod_1.4.21.tar.gz</package>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DEXSeq_1.14.2.tar.gz</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="DEXSEQ_ROOT">$INSTALL_DIR/DEXSeq/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            DEXSeq in version
+        </readme>
+    </package>
+</tool_dependency>