# HG changeset patch
# User stef
# Date 1412675813 14400
# Node ID def7829bec8439876ce8fe3d3ee05043d7a205f4
# Parent  bbfcf3187538d5ab85956b6eb4a6bf49e78e473e
Uploaded

diff -r bbfcf3187538 -r def7829bec84 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 06 11:19:41 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 07 05:56:53 2014 -0400
@@ -13,11 +13,36 @@
 					<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://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_1.32.4.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_3.20.5.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>
+					<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_1.22.9.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>
+					
 					<!--
 					<package>http://path/to/R.methodsS3_1.6.1.tar.gz</package>
 					<package>http://path/to/matrixStats_0.10.0.tar.gz</package>