Mercurial > repos > stef > qdnaseq_test
changeset 12:6936ad89f369 draft
Uploaded
| author | stef |
|---|---|
| date | Thu, 06 Nov 2014 04:21:49 -0500 |
| parents | 4fe3844a5fb0 |
| children | f8b16dd1ecb7 |
| files | QDNAseq.R |
| diffstat | 1 files changed, 19 insertions(+), 11 deletions(-) [+] |
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--- a/QDNAseq.R Thu Nov 06 03:57:21 2014 -0500 +++ b/QDNAseq.R Thu Nov 06 04:21:49 2014 -0500 @@ -135,24 +135,32 @@ ## ================================================== ## Start of analysis ## ================================================== -cmdLineArgs <- commandArgs(TRUE) -config <- cmdLineArgs[1] -installDir <- cmdLineArgs[2] - -MAIN_NAME <- '[INFO] ' -TOOL_PATH <- getScriptPath() -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' - catMsg( "Starting QDNAseq wrapper" ) 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] +TOO_PATH <- cmdLineArgs[2] + +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' + ## sourcing the config file will load all input params ## many variables are imported via sourced "config" source( config )