# HG changeset patch
# User testtool
# Date 1493044280 14400
# Node ID 660897ee0d12db3f13acefb54f35401602595d0a
# Parent  4987433afb56d6afe6e8eddb65cc55a2f5a5e403
Uploaded

diff -r 4987433afb56 -r 660897ee0d12 GRsetFromGEO/GRsetFromGEO.R
--- a/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:09:39 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:31:20 2017 -0400
@@ -1,9 +1,10 @@
-require("BiocGenerics", quietly = TRUE)
-require("data.table", quietly = TRUE)
 require("GEOquery", quietly = TRUE)
 require("minfi", quietly = TRUE)
 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
 
+options(warn = -1)
+options("download.file.method"="wget")
+
 args <- commandArgs(trailingOnly = TRUE)
 GSE = args[1] 
 output = args[2] 
@@ -26,7 +27,13 @@
 mergeManifest = FALSE
 i = 1
 
-gset <- GEOquery::getGEO(GSE)
+gset <- getGEO(GSE)
+
+if (is.null(GSE)) {
+  stop("Must specify GSE")
+} else {
+  options(download.file.method.GEOquery = "wget")}
+  
 gset <- gset[[1]]
 
 platform <- annotation(gset)
diff -r 4987433afb56 -r 660897ee0d12 GRsetFromGEO/tool_dependencies.xml
--- a/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:09:39 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:31:20 2017 -0400
@@ -6,6 +6,10 @@
                   <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://bioarchive.galaxyproject.org/minfi_1.21.6.tar.gz</package>
+
+                   <package>https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz</package>
+
                       <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">
                           https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz
                       </package>