diff QDNAseq.R @ 9:4efd258b33d9 draft

Uploaded

--- a/QDNAseq.R	Mon Oct 27 05:38:16 2014 -0400
+++ b/QDNAseq.R	Fri Oct 31 07:13:53 2014 -0400
@@ -135,9 +135,13 @@
 ## ==================================================
 ## Start of analysis
 ## ==================================================
+cmdLineArgs <- commandArgs(TRUE)
+config      <- cmdLineArgs[1]
+installDir  <- cmdLineArgs[2]
+
 MAIN_NAME <- '[INFO] '
 TOOL_PATH <- getScriptPath()
-CSS_FILE  <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
+CSS_FILE  <- paste( installDir, '/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'
@@ -146,20 +150,9 @@
 catMsg( "Loading R libraries" )
 catMsg( R.version.string )
 
-packs <- c( "limma", "marray", "CGHbase", "impute", "DNAcopy", "CGHcall" )
-for ( pack in packs ){
-	catMsg( c("Loading ", pack) )
-	library( pack )
-}
-
-## 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]
-
 ## sourcing the config file will load all input params
 ## many variables are imported via sourced "config"
 source( config )