# HG changeset patch
# User testtool
# Date 1493046937 14400
# Node ID 591f68d46899baba7472a779e1244710b39127ea
# Parent  28416ed17e4175d3c3b2983c0ebac0c787ef3b05
Uploaded

diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/GRsetFromGEO.xml
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Apr 24 10:52:54 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Apr 24 11:15:37 2017 -0400
@@ -4,7 +4,6 @@
   </description>
   <requirements>
     <requirement type="package" version="3.2.1">R</requirement>
-    <requirement type="package" version="1.16.0">minfi</requirement>
      </requirements>
 <stdio>
    <exit_code range="1:" />
diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/Untitled.R
--- a/GRsetFromGEO/Untitled.R	Mon Apr 24 10:52:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-require("minfi", quietly = TRUE)
-
-args <- commandArgs(trailingOnly = TRUE)
-GSE = args[1] 
-output = args[2] 
-
-GRset <- getGenomicRatioSetFromGEO(GSE)
-
-save(GRset,output)
-
diff -r 28416ed17e41 -r 591f68d46899 GRsetFromGEO/tool_dependencies.xml
--- a/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:52:54 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 11:15:37 2017 -0400
@@ -1,10 +1,103 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="minfi" version="1.16.0">
-    	# TODO:
-        <repository changeset_revision="d0cee75b3e2e" name="package_minfi_1_16_0" owner="nturaga" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="libcurl" version="7.35">
+        <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.2.1">
-        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="minfi" version="1.16.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libcurl" version="7.35" />
+                    </repository>
+                    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.2.1" />
+                    </repository>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/matrixStats_0.14.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/registry_0.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.9.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringi_1.0-1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/magrittr_1.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringr_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/pkgmaker_0.22.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rngtools_1.2.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/doRNG_1.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RSQLite_1.0.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/bitops_1.0-6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RCurl_1.95-4.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/XML_3.98-1.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/lambda.r_1.1.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.options_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.logger_1.4.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/snow_0.3-13.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/BiocParallel_1.3.54.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Rsamtools_1.22.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/GenomicAlignments_1.6.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/rtracklayer_1.30.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/biomaRt_2.26.1.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicFeatures_1.22.13.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/bumphunter_1.10.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/beanplot_1.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/nor1mix_1.2-1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/multtest_2.26.0.tar.gz</package>
+                    <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/siggenes_1.44.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.32.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/base64_1.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.12.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mclust_5.0.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.52.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/Rcpp_0.12.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/plyr_1.8.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/reshape_0.8.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/quadprog_1.5-5.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/GEOquery_2.35.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/colorspace_1.2-6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/dichromat_2.0-0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/labeling_0.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/munsell_0.4.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/reshape2_1.4.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/gtable_0.2.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/scales_0.4.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/ggplot2_2.1.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rgl_0.95.1441.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/ellipse_0.3-8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/corpcor_1.6.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/cluster_2.0.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/gridBase_0.4-7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/doParallel_1.0.10.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/NMF_0.20.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/irlba_2.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/igraph_1.0.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mixOmics_5.2.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/minfi_1.16.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/getopt_1.20.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/data/experiment/src/contrib/FlowSorted.Blood.450k_1.8.0.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
     </package>
 </tool_dependency>