# HG changeset patch
# User testtool
# Date 1493984204 14400
# Node ID 543137e0cda5fa8aaabab8bd9e47f5b4f50f5097
# Parent  4f4ff04de29797411e005715c0f19d5d4e731e86
Uploaded

diff -r 4f4ff04de297 -r 543137e0cda5 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 05 07:16:21 2017 -0400
+++ b/tool_dependencies.xml	Fri May 05 07:36:44 2017 -0400
@@ -17,25 +17,38 @@
                       <package name="R" version="3.2.1" />
                     </repository>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.22.0.tar.gz</package>
+                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.1.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>
-                    <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/XVector_0.10.0.tar.gz</package>
-                    <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/GenomeInfoDb_1.12.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/zlibbioc_1.22.0.tar.gz</package>
-                    <package>https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/XVector_0.10.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/Biostrings_2.44.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/lattice_0.20-35.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz</package>
+                    <package>https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://cran.rstudio.com/src/contrib/matrixStats_0.52.2.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.32.2.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/registry_0.3.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/stringi_1.1.5.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/stringr_1.2.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/doRNG_1.6.6.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/DBI_0.6-1.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/RSQLite_1.1-2.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/RCurl_1.95-4.8.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/XML_3.98-1.7.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.10.1.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/lattice_0.20-35.tar.gz</package>
                     <package>https://bioc.ism.ac.jp/packages/3.3/bioc/src/contrib/SummarizedExperiment_1.2.3.tar.gz</package>
-                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.1.tar.gz</package>
-                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/Biostrings_2.44.0.tar.gz</package>
-                    <package>https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.58.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/GenomicFeatures_1.28.0.tar.gz</package>
-                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.10.1.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/doRNG_1.6.6.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/stringr_1.2.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/biomaRt_2.32.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.10.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/base64_2.0.tar.gz</package>
@@ -45,35 +58,22 @@
                     <package>https://cran.r-project.org/src/contrib/Matrix_1.2-10.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/R6_2.2.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/nlme_3.1-131.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/XML_3.98-1.7.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
-                    <package>https://cran.rstudio.com/src/contrib/matrixStats_0.52.2.tar.gz</package>
-                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/annotate_1.54.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/nor1mix_1.2-2.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/RCurl_1.95-4.8.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/data.table_1.10.4.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/mclust_5.2.3.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/survival_2.41-3.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/registry_0.3.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.18.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/openssl_0.9.6.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/Rsamtools_1.28.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/RSQLite_1.1-2.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/httr_1.2.1.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/GenomicAlignments_1.12.0.tar.gz</package>
                     <package>ftp://164.41.45.6/pub/plan/R/src/contrib/beanplot_1.2.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/DBI_0.6-1.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/memoise_1.1.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.38.0.tar.gz</package>
-                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.32.2.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/GEOquery_2.42.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/MASS_7.3-47.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/reshape_0.8.6.tar.gz</package>