Mercurial > repos > stef > qdnaseq_test

comparison QDNAseq.R @ 12:6936ad89f369 draft

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Uploaded
author stef
date Thu, 06 Nov 2014 04:21:49 -0500
parents 4efd258b33d9
children b711e34e73dc
comparison
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11:4fe3844a5fb0 12:6936ad89f369
133 133
134 134
135 ## ================================================== 135 ## ==================================================
136 ## Start of analysis 136 ## Start of analysis
137 ## ================================================== 137 ## ==================================================
138 catMsg( "Starting QDNAseq wrapper" )
139 catMsg( "Loading R libraries" )
140 catMsg( R.version.string )
141
142 packs <- c( "limma", "marray", "CGHbase", "impute", "DNAcopy", "CGHcall" )
143 for ( pack in packs ){
144 catMsg( c("Loading ", pack) )
145 library( pack )
146 }
147
148 ## supress msg to allow R to finish with non-error msg
149 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
150 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
151
152 ## only one param: the tmp config file
138 cmdLineArgs <- commandArgs(TRUE) 153 cmdLineArgs <- commandArgs(TRUE)
139 config <- cmdLineArgs[1] 154 config <- cmdLineArgs[1]
140 installDir <- cmdLineArgs[2] 155 TOO_PATH <- cmdLineArgs[2]
141 156
142 MAIN_NAME <- '[INFO] ' 157 MAIN_NAME <- '[INFO] '
143 TOOL_PATH <- getScriptPath() 158 #TOOL_PATH <- getScriptPath()
144 CSS_FILE <- paste( installDir, '/static/css/QDNAseq.css', sep="" ) 159 CSS_FILE <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" )
145 DECIMALS <- 3 160 DECIMALS <- 3
146 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' 161 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
147 PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css' 162 PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
148
149 catMsg( "Starting QDNAseq wrapper" )
150 catMsg( "Loading R libraries" )
151 catMsg( R.version.string )
152
153 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
154 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
155 163
156 ## sourcing the config file will load all input params 164 ## sourcing the config file will load all input params
157 ## many variables are imported via sourced "config" 165 ## many variables are imported via sourced "config"
158 source( config ) 166 source( config )
159 167