# HG changeset patch
# User stef
# Date 1415198880 18000
# Node ID f44792741a2f589ea68cf15691adc6a79b77a27b
# Parent  4a3ff383a68012cb0123d24f6dd2be4c9fb1cabb
Uploaded

diff -r 4a3ff383a680 -r f44792741a2f tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 27 06:39:51 2014 -0400
+++ b/tool_dependencies.xml	Wed Nov 05 09:48:00 2014 -0500
@@ -1,55 +1,36 @@
 <?xml version="1.0"?>
 <tool_dependency>
 
+	<!--
 	<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" />
+		<repository name="package_r_3_1_0" owner="iuc" prior_installation_required="True" />
 	</package>
+	-->
+	<package name="R" version="3.1.1">
+		<repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" 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="shell_command">echo "[DEBUG] Starting install actions"</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">
+					<!--
+					<repository name="package_r_3_1_0" owner="iuc">
 						<package name="R" version="3.1.0" />
 					</repository>
-					<!--
-					<package>http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package>
-					<package>http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.20.9.tar.gz</package>
-					<package>http://bioconductor.org/packages/release/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package>
-				-->
-					<!--
-					<package>http://cran.fhcrc.org/src/contrib/R.methodsS3_1.6.1.tar.gz</package>
-					<package>http://cran.fhcrc.org/src/contrib/matrixStats_0.10.0.tar.gz</package>
-					<package>http://cran.fhcrc.org/src/contrib/R.oo_1.18.0.tar.gz</package>
-					<package>http://cran.fhcrc.org/src/contrib/R.utils_1.33.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocGenerics_0.10.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biobase_2.24.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/limma_3.20.9.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/marray_1.42.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHbase_1.24.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/impute_1.38.1.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/DNAcopy_1.38.1.tar.gz</package>
 					-->
 
+					<repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="R" version="3.1.1" />
+					</repository>
+					
 					<!--
-					<package>http://cran.fhcrc.org/src/contrib/snow_0.3-13.tar.gz</package>
-					<package>http://cran.fhcrc.org/src/contrib/snowfall_1.84-6.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/CGHcall_2.26.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/IRanges_1.22.10.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomeInfoDb_1.0.2.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/XVector_0.4.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.16.4.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/zlibbioc_1.10.0.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Biostrings_2.32.1.tar.gz</package>
-					<package>http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsamtools_1.16.1.tar.gz</package>
-					<package>http://bioconductor.org/packages/2.14/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</package>
+					<action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</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>
@@ -74,6 +55,9 @@
 					<package>http://path/to/Rsamtools_1.16.1.tar.gz</package>
 					<package>http://path/to/QDNAseq_1.0.5.tar.gz</package>
 					-->
+					<!-- HERE all the packages hosted at bitbucket -->
+					<!-- currently breaks at DNAcopy -->
+					
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package>
@@ -102,7 +86,7 @@
 					-->
 
 				</action>
-				<action type="shell_command">echo "[DEBUG] ...after"</action>
+				<action type="shell_command">echo "[DEBUG] ...done with install actions"</action>
 			</actions>
 		</install>
 		<readme>