# HG changeset patch
# User testtool
# Date 1493042979 14400
# Node ID 4987433afb56d6afe6e8eddb65cc55a2f5a5e403
# Parent  1ed398538e91a22b962b48f88935a8345508c1ad
Uploaded

diff -r 1ed398538e91 -r 4987433afb56 GRsetFromGEO/GRsetFromGEO.R
--- a/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:04:18 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:09:39 2017 -0400
@@ -1,5 +1,7 @@
+require("BiocGenerics", quietly = TRUE)
+require("data.table", quietly = TRUE)
+require("GEOquery", quietly = TRUE)
 require("minfi", quietly = TRUE)
-require("GEOquery", quietly = TRUE)
 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
 
 args <- commandArgs(trailingOnly = TRUE)
@@ -24,7 +26,7 @@
 mergeManifest = FALSE
 i = 1
 
-gset <- getGEO(GSE)
+gset <- GEOquery::getGEO(GSE)
 gset <- gset[[1]]
 
 platform <- annotation(gset)
diff -r 1ed398538e91 -r 4987433afb56 GRsetFromGEO/tool_dependencies.xml
--- a/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:04:18 2017 -0400
+++ b/GRsetFromGEO/tool_dependencies.xml	Mon Apr 24 10:09:39 2017 -0400
@@ -1,5 +1,6 @@
-<?xml version='1.0' encoding='utf-8' ?>
+<?xml version="1.0"?>
 <tool_dependency>
+  <install version="1.0">
     <actions>
                 <action type="setup_r_environment">
                   <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -267,11 +268,6 @@
                           https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz
                       </package>
                   </action>
-                  <action type="download_by_url" >
-    https://depot.galaxyproject.org/software/bioconductor-minfi/bioconductor-minfi_1.20.0_src_all.tar.gz
-</action>
-<action type="download_by_url" >
-    https://depot.galaxyproject.org/software/bioconductor-geoquery/bioconductor-geoquery_2.38.4_src_all.tar.gz
-</action>
               </actions>
+              </install>
             </tool_dependency>