# HG changeset patch
# User nturaga
# Date 1461082861 14400
# Node ID 3cd8ea4f7079e41974c4370bf86d6a41ffbd3776
# Parent  8b26eeb2da292cb6476ae066b1518a5ef40d0fba
planemo upload commit fb90aafc93e5e63acfcdac4c27cfd865cdf06c5a-dirty

diff -r 8b26eeb2da29 -r 3cd8ea4f7079 minfi_pipeline.R
--- a/minfi_pipeline.R	Tue Apr 19 11:11:16 2016 -0400
+++ b/minfi_pipeline.R	Tue Apr 19 12:21:01 2016 -0400
@@ -4,6 +4,8 @@
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
+install.packages('getopt', repos='http://cran.us.r-project.org')
+
 library("getopt")
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
 args <- commandArgs(trailingOnly = TRUE)
diff -r 8b26eeb2da29 -r 3cd8ea4f7079 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 19 11:11:16 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 19 12:21:01 2016 -0400
@@ -2,7 +2,7 @@
 <tool_dependency>
     <package name="minfi" version="1.16.0">
     	# TODO:
-        <repository changeset_revision="f453b1c037bc" name="package_minfi_1_16_0" owner="nturaga" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d0cee75b3e2e" name="package_minfi_1_16_0" owner="nturaga" 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" />