# HG changeset patch
# User testtool
# Date 1486562295 18000
# Node ID 315b0dc61049dbfdc15ad97ae2bc239443fdef9a
# Parent  c9ab017e40b5bb2c3c9abd7b2c6958e50d718c6a
Uploaded

diff -r c9ab017e40b5 -r 315b0dc61049 getGEO/.RData
Binary file getGEO/.RData has changed
diff -r c9ab017e40b5 -r 315b0dc61049 getGEO/.Rhistory
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/.Rhistory	Wed Feb 08 08:58:15 2017 -0500
@@ -0,0 +1,17 @@
+first<-getGEO(TAB$ID[1],getGPL=FALSE)
+require("BiocGenerics",quietly = TRUE)
+require("data.table",quietly = TRUE)
+require("minfi",quietly = TRUE)
+require("ChIPseeker",quietly = TRUE)
+require("ChIPpeakAnno",quietly = TRUE)
+require("TxDb.Hsapiens.UCSC.hg19.knownGene",quietly = TRUE)
+require("FDb.InfiniumMethylation.hg19",quietly = TRUE)
+require("GEOquery",quietly = TRUE)
+require("rtracklayer",quietly = TRUE)
+install.packages("formatR")
+library(formatR)
+getwd()
+tidy_eval("/Users/katarzynamurat/Desktop/galaxy/tools/getGEO")
+tidy_eval("/Users/katarzynamurat/Desktop/galaxy/tools/getGEO")
+source('~/Desktop/galaxy/tools/findDMR/findDMR.R')
+source('~/Desktop/galaxy/tools/findDMR/findDMR.R')
diff -r c9ab017e40b5 -r 315b0dc61049 getGEO/getGEO.R
--- a/getGEO/getGEO.R	Mon Feb 06 10:39:59 2017 -0500
+++ b/getGEO/getGEO.R	Wed Feb 08 08:58:15 2017 -0500
@@ -5,6 +5,7 @@
 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
 
 options(warn = -1)
+options("download.file.method"="wget")
 args <- commandArgs(trailingOnly = TRUE)
 GSMTable = args[1]
 MetaTable = args[2]
diff -r c9ab017e40b5 -r 315b0dc61049 getGEO/getGEO.xml
--- a/getGEO/getGEO.xml	Mon Feb 06 10:39:59 2017 -0500
+++ b/getGEO/getGEO.xml	Wed Feb 08 08:58:15 2017 -0500
@@ -1,10 +1,12 @@
 <tool id="GEO" name="getGEO" version="1.16.2">
-  <description>
-  samples records
-  </description>
+  <?xml version='1.0' encoding='utf-8'?>
   <requirements>
-         <requirement type="package" version="3.2.1">R</requirement>
-     </requirements>
+    <tool_dependency>
+          <package name="R" version="3.2.1">
+              <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+          </package>
+        </tool_dependency>
+</requirements>
 <stdio>
    <exit_code range="1:" />
 </stdio>
diff -r c9ab017e40b5 -r 315b0dc61049 getGEO/tool_dependencies.xml
--- a/getGEO/tool_dependencies.xml	Mon Feb 06 10:39:59 2017 -0500
+++ b/getGEO/tool_dependencies.xml	Wed Feb 08 08:58:15 2017 -0500
@@ -1,279 +1,6 @@
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-                          https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz
-                      </package>
-                      <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">
-                          https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz
-                      </package>
-                      <package sha256sum="d47be4430a1c343c20f9d3f67b8511506904e46be13ea4199769f012f1449209">
-                          https://depot.galaxyproject.org/software/GO.db/GO.db_3.4.0.tar.gz
-                      </package>
-                      <package sha256sum="dfccd4b4d6ec90cd7628fd128d2456d792f406cee4d32b13448dcb0ffe4ab056">
-                          https://depot.galaxyproject.org/software/NMF/NMF_0.20.6.tar.gz
-                      </package>
-                      <package sha256sum="7fa594d9576592e393283ec4fc79fd72128f663bd516e05651957ce1e6fe3c38">
-                          https://depot.galaxyproject.org/software/colorspace/colorspace_1.3-1.tar.gz
-                      </package>
-                      <package sha256sum="31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1">
-                          https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0.tar.gz
-                      </package>
-                      <package sha256sum="7a4957c66ff622d7d1456adfbb728c60d406cdb2a754979797f9dcb0dc8fee99">
-                          https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz
-                      </package>
-                      <package sha256sum="5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1">
-                          https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz
-                      </package>
-                      <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">
-                          https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz
-                      </package>
-                      <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">
-                          https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz
-                      </package>
-                      <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">
-                          https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz
-                      </package>
-                  </action>
-              </actions>
-          <readme>
-          </readme>
-  </tool_dependency>
+<tool_dependency>
+  <package name="R" version="3.2.1">
+      <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>