# HG changeset patch
# User stef
# Date 1403172014 14400
# Node ID ce31fec9c3d5ea53a7bb27c4da32ba780a71924c

Uploaded

diff -r 000000000000 -r ce31fec9c3d5 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 19 06:00:14 2014 -0400
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<!--
+    <package name="R" version="3.1.0">
+        <repository name="package_r_3_1_0" owner="" prior_installation_required="True" />
+    </package>
+    <package name="qdnaseq" version="1.0.5">
+        <install version="1.0">
+            <actions>
+				<action type="shell_command">echo "[DEBUG] ..."</action>
+                <action type="setup_r_environment">
+					
+                    <repository name="package_r_3_1_0" owner="">
+                        <package name="R" version="3.1.0" />
+                    </repository>
+                    
+                    <package>http://path/to/R.methodsS3_1.6.1.tar.gz</package>
+					<package>http://path/to/matrixStats_0.10.0.tar.gz</package>
+					<package>http://path/to/R.oo_1.18.0.tar.gz</package>
+					<package>http://path/to/R.utils_1.32.4.tar.gz</package>
+					<package>http://path/to/BiocGenerics_0.10.0.tar.gz</package>
+					<package>http://path/to/Biobase_2.24.0.tar.gz</package>
+					<package>http://path/to/limma_3.20.5.tar.gz</package>
+					<package>http://path/to/marray_1.42.0.tar.gz</package>
+					<package>http://path/to/CGHbase_1.24.0.tar.gz</package>
+					<package>http://path/to/impute_1.38.1.tar.gz</package>
+					<package>http://path/to/DNAcopy_1.38.1.tar.gz</package>
+					<package>http://path/to/snow_0.3-13.tar.gz</package>
+					<package>http://path/to/snowfall_1.84-6.tar.gz</package>
+					<package>http://path/to/CGHcall_2.26.0.tar.gz</package>
+					<package>http://path/to/IRanges_1.22.9.tar.gz</package>
+					<package>http://path/to/GenomeInfoDb_1.0.2.tar.gz</package>
+					<package>http://path/to/XVector_0.4.0.tar.gz</package>
+					<package>http://path/to/GenomicRanges_1.16.3.tar.gz</package>
+					<package>http://path/to/zlibbioc_1.10.0.tar.gz</package>
+					<package>http://path/to/Biostrings_2.32.0.tar.gz</package>
+					<package>http://path/to/bitops_1.0-6.tar.gz</package>
+					<package>http://path/to/Rsamtools_1.16.1.tar.gz</package>
+					<package>http://path/to/QDNAseq_1.0.5.tar.gz</package>
+					
+                </action>
+            </actions>
+        </install>
+        <readme>
+			Prepares R Bioconductor package "QDNAseq" and all of its dependencies.
+		</readme>
+    </package>
+	-->
+</tool_dependency>