# HG changeset patch
# User stef
# Date 1412606836 14400
# Node ID 8473e3b3c386fc5f7b2c0129b830b1973cdf2610
# Parent  42096296e06fc50bb2a9505d593e295be1f080ec
Uploaded

diff -r 42096296e06f -r 8473e3b3c386 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 06 10:30:19 2014 -0400
+++ b/tool_dependencies.xml	Mon Oct 06 10:47:16 2014 -0400
@@ -1,27 +1,53 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
+
+	<package name="R" version="3.1.0">
+		<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="qdnaseq" version="1.0.5">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">echo "[DEBUG] ...before"</action>
+				<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>
+					
+					<package>http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.9REMOVE.tar.gz</package>
 
-    <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" -->
-    <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" -->
-    
-    <package name="R" version="3.1.0">
-        <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="qdnaseq" version="1.0.5">
-        <repository name="package_qdnaseq_1_0_5" owner="stef"/>
-    </package>
-    -->
-
-    <!--
-    <action type="set_environment">
-        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-    </action>
-    -->
-    
+					<!--
+					<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>
+				<action type="shell_command">echo "[DEBUG] ...after"</action>
+			</actions>
+		</install>
+		<readme>
+			Prepares R Bioconductor package "QDNAseq" and all of its dependencies.
+		</readme>
+	</package>
 </tool_dependency>