# HG changeset patch
# User stef
# Date 1412605819 14400
# Node ID 42096296e06fc50bb2a9505d593e295be1f080ec
# Parent  3fcdbbc43d6261febb3646d016006c5f64a0c782
Uploaded

diff -r 3fcdbbc43d62 -r 42096296e06f tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 19 06:02:41 2014 -0400
+++ b/tool_dependencies.xml	Mon Oct 06 10:30:19 2014 -0400
@@ -1,49 +1,27 @@
 <?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>
-	-->
+    
+    <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>
+
+    <!-- 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>
+    -->
+    
 </tool_dependency>