# HG changeset patch
# User stef
# Date 1415264010 18000
# Node ID 14491b8d4d2b67ca434abaf62b4a0ff397637872
# Parent  df8b1d258e35d908b068b1099ccb6e5eeb36238d
Uploaded

diff -r df8b1d258e35 -r 14491b8d4d2b tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 05 11:21:00 2014 -0500
+++ b/tool_dependencies.xml	Thu Nov 06 03:53:30 2014 -0500
@@ -16,12 +16,14 @@
 				<action type="shell_command">echo "[DEBUG] Starting install actions"</action>
 				<action type="setup_r_environment">
 					
+					<!-- originally tried 3_1_0 but multiple errors -->
 					<!--
 					<repository name="package_r_3_1_0" owner="iuc">
 						<package name="R" version="3.1.0" />
 					</repository>
 					-->
 
+					<!-- this one has to compile but works in all tests I did -->
 					<repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
 						<package name="R_3_1_1" version="3.1.1" />
 					</repository>
@@ -30,34 +32,8 @@
 					<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>
-					<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>
-					-->
 					<!-- HERE all the packages hosted at bitbucket -->
-					<!-- currently breaks at DNAcopy -->
-					
+					<!-- currently breaks at DNAcopy with R3.1.0 iuc dep pack -->
 					<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>
@@ -68,9 +44,6 @@
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package>
-					
-					
-					
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package>
@@ -84,7 +57,6 @@
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package>
 					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package>
-					
 
 				</action>
 				<action type="shell_command">echo "[DEBUG] ...done with install actions"</action>