diff QDNAseq.R @ 74:0feb7fa37245 draft

Uploaded

--- a/QDNAseq.R	Fri Oct 24 07:06:55 2014 -0400
+++ b/QDNAseq.R	Thu Nov 06 05:09:17 2014 -0500
@@ -135,23 +135,26 @@
 ## ==================================================
 ## Start of analysis
 ## ==================================================
+## ==================================================
+## Start of analysis
+## ==================================================
 MAIN_NAME <- '[INFO] '
-TOOL_PATH <- getScriptPath()
-CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
-DECIMALS  <- 3
-WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
-PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
-
 catMsg( "Starting QDNAseq wrapper" )	
 catMsg( "Loading R libraries" )
 catMsg( R.version.string )
 
+## supress msg to allow R to finish with non-error msg
 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
 
 ## only one param: the tmp config file
 cmdLineArgs <- commandArgs(TRUE)
 config      <- cmdLineArgs[1]
+TOOL_PATH   <- cmdLineArgs[2]
+CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
+DECIMALS  <- 3
+WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
+PURE_CSS  <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
 
 ## sourcing the config file will load all input params
 ## many variables are imported via sourced "config"