view QDNAseq.R @ 76:4588384edba1 draft

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#!/usr/bin/Rscript

## --------------------
## prints all arguments as msg
## --------------------
catMsg <- function( msg=c() ){	
	cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
}
## --------------------
## return the location of this script
## --------------------
getScriptPath <- function(){
    cmd.args <- commandArgs()
    m <- regexpr("(?<=^--file=).+", cmd.args, perl=TRUE)
    script.dir <- dirname(regmatches(cmd.args, m))
    if( length(script.dir) == 0 ) stop("[ERR] Can't determine script dir: please call the script with Rscript\n")
    if( length(script.dir) > 1 ) stop("[ERR] Can't determine script dir: more than one '--file' argument detected\n")
    return(script.dir)
}
## --------------------
## Some html creation functions
## --------------------
htmlTableRow <- function( string_array=c() ){
	td_cells <- ''
	for ( i in string_array ){ 
		td_cells <- paste( td_cells, '<td>', i, '</td>', sep='' )	
	}
	return( paste( "<tr>", td_cells, "</tr>") )
}
htmlLink <- function( path, desc="LINK" ){
	return( paste( '<a href="', path, '">', desc, "</a>", sep='') )
}
## --------------------
## constructs a list with input bam file info
## --------------------
makeBamFileList <- function( paths, names ){	
	tmp <- list()
	l1 <- length(paths)
	l2 <- length(names)
	if ( l1 != l2 ) stop( "Unequal amount of bam-paths (", l1, ") and -names (", l2, ") in makeBamFileList!!!\n" )
	if ( l1 == 0 ){ return(tmp) } # empty list in debug mode

	for ( i in 1:length(paths) ){
		path <- paths[i]
		name <- names[i]
		file <- basename(path)

		tmp[[ file ]] <- name
		tmp[[ 'all_paths' ]] <- c( tmp[[ 'all_paths' ]], path )
		tmp[[ 'all_files' ]] <- c( tmp[[ 'all_files' ]], file )
		tmp[[ 'all_names' ]] <- c( tmp[[ 'all_names' ]], name )
	}
	return( tmp )
}

## --------------------
## copied code for extracting the regions by segment call status
## --------------------
fuseRegions <- function( obj, minRatio=0 ) {
	if ( ncol(obj) > 1 ) stop('Please specify which sample...')

	data <- data.frame( obj@featureData@data[,1:3], copynumber(obj), segmented(obj), check.names=FALSE, stringsAsFactors=FALSE)
	colnames( data ) <- c( "chr", "start", "end", "log2", "segmentval" )
	
	fused.data <- data.frame()
	curr.bin <- 1
	for ( chr in unique( data$chr ) ) {
		chr.data  <- data[ data$chr == chr, ]
		prev.bin  <- curr.bin
		prev.log2 <- chr.data[ 1, 'log2' ]
		prev.segm <- chr.data[ 1, 'segmentval' ]
		start     <- chr.data[ 1, 'start' ]

		if ( nrow(chr.data) > 1) {
			for ( i in 2:nrow(chr.data) ) {
				curr.bin  <- curr.bin + 1
				curr.segm <- chr.data[ i, 'segmentval']

				if ( curr.segm != prev.segm ) {
					fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
					prev.segm <- curr.segm
					prev.bin  <- curr.bin
					start     <- chr.data[ i, 'start']
				}
			}
			fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
		}else{
			fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], segmentval=round(prev.segm, digits=DECIMALS) ) )
		}
	}
	## remove regions with low amplitude
	fused.data <- fused.data[ abs(fused.data$segmentval) >= minRatio, ]
	fused.data
}

## DESC: takes the output of fuse.regions and outputs a txt file per sample
outputRegionsFromList <- function ( regionsList, outputBasename, outputDir="./", binSize, storeList ){
	if ( missing(regionsList) ) stop( 'Please provide regionsList...' )
	if ( missing(outputBasename) ) stop( 'Please provide outputBasename...' )
	if ( !is.list(regionsList) ) stop( 'Input not a list...?' )
	if ( length(regionsList) < 1 ) stop( 'List seems empty...?' )
	if ( file.exists( outputDir ) ) catMsg( c(" Using dir ", outputDir, " for output") )
	else dir.create( outputDir )

	## have to set R output options otherwise scientific method is used at some point
	options( "scipen"=100 )

	sampleCount <- length( regionsList )
	sampleNames <- names( regionsList )
	bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )
	
	catMsg( c( " There are ", sampleCount, " samples found in input list") )

	for ( sample in sampleNames ){		
		catMsg( c(" Working on sample ", sample ) )
		regionCount <- nrow( regionsList[[sample]] )
		
		outSampleBase   <- paste( outputBasename, '_', sample, '_', binSize, 'kbp', sep='')
		outBedgraphFile <- paste( outSampleBase, '.bedGraph', sep="" )
		outBedgraphPath <- paste( outputDir, '/', outBedgraphFile, sep="" )

		## ---------- BEDGRAPH ----------
		txt <- paste( "track type=bedGraph color=0,100,0 altColor=255,0,0 name=", sample," description=segmented_regions_from_QDNAseq_",binSize,"kbp\n", sep="")
		sink( outBedgraphPath )
			cat( txt )
		sink()
		write.table( regionsList[[sample]][,bedgraphColumns], outBedgraphPath, quote=F, sep="\t", row.names=F, append=T, col.names=F)
		#outFiles[[sample]] <- c( outBedgraphFile )
		storeList[[ paste( binSize, sample, 'bedgraph', sep="_")]] <- outBedgraphFile
	}
	return(storeList)
}


## ==================================================
## Start of analysis
## ==================================================
MAIN_NAME <- '[INFO] '
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"
source( config )

## desparate tries to make png text scale well, damn you R...!
PLOT_RES  <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 6.3 
PAR_SET   <- list( pch=22 )

systemUser <- system("whoami",T)
qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
rVersion <- R.version.string
startTime <- Sys.time()
analysisStart <- as.character( startTime )
catMsg( c("QDNAseq version: ", qdnaseqVersion) )
catMsg( c( rVersion ) )

## get the comma separated list of chromosomes to exclude
excludeChrs <- unlist( strsplit( excludeChrsString, ",") )
binSizes <- as.numeric( unlist( strsplit( binSizesString, ",") ) )


## ------------------------
## DEBUG
if ( debug ){
	catMsg( c("Analysis run by user: ", systemUser ) )
	catMsg( c("DEBUG SessionInfo: " ) )
	print( sessionInfo() )
}
## /DEBUG
## ------------------------

## prepare output dir
if ( !file.exists( outputPath) ){
	dir.create( outputPath )
}

## copy source config file to output dir to include it in output zip
if ( inGalaxy ){
	file.copy( config, paste(outputPath, 'galaxyConfigFile.R', sep='/') )	
}

## setup bam filelist for easy retrieval later
fileList    <- makeBamFileList( bamsPaths, bamsNames )
bamCount    <- length( fileList[[ 'all_paths' ]] )

gzipOutputName <- paste( 'QDNAseqResults_', outputName, '.zip', sep='' )
gzipOutputPath <- paste( outputPath, '/', gzipOutputName, sep='')
htmlOutputName <- 'index.html'
htmlOutputPath <- paste( outputPath, '/', htmlOutputName, sep='')

plotted_images <- list() # to keep track of images for later linking
regions <- list() # will contain the segments
outputFiles <- list()

## ------------------------
## in case of debug just use inbuilt LGG data for speedup
if ( debug ){ 
	binSizes <- c(15)
	bamsPaths  <- c( "BUILD_IN_DATA")
	bamsNames  <- c( "LGG150")
	fileList   <- makeBamFileList( bamsPaths, bamsNames )
	bamCount   <- length( fileList[[ 'all_paths' ]] )
}

for ( binSize in binSizes ){

	## ------------------------
	## construct output file-names and -paths
	## ------------------------
	robjReadCoName <- paste( binSize, 'kbp_QDNAseqReadCounts.rds', sep='')
	robjCopyNrName <- paste( binSize, 'kbp_QDNAseqCopyNumbers.rds', sep='')
	igvCopyNrName  <- paste( binSize, 'kbp_QDNAseqCopyNumbers.igv', sep='')
	robjSegmntName <- paste( binSize, 'kbp_QDNAseqCopyNumbersSegmented.rds', sep='')
	regiOutputName <- paste( binSize, 'kbp_QDNAseqRegions.rds', sep='')
	noiseImgName   <- paste( binSize, 'kbp_QDNAseqNoiseplot.png', sep='')
	
	robjReadCoPath <- paste( outputPath, '/', robjReadCoName, sep='')
	robjCopyNrPath <- paste( outputPath, '/', robjCopyNrName, sep='')
	robjSegmntPath <- paste( outputPath, '/', robjSegmntName, sep='')
	robjRegionPath <- paste( outputPath, '/', regiOutputName, sep='')
	igvCopyNrPath  <- paste( outputPath, '/', igvCopyNrName, sep='')
	noiseImgPath   <- paste( outputPath, '/', noiseImgName, sep='')

	binAnnFile <- paste( TOOL_PATH, '/static/binannotation/', binSize, 'kbp_binAnnotations.rds', sep="" )
	if ( file.exists(binAnnFile) ){
		binAnnotations <- readRDS( binAnnFile )
		catMsg( c("Using local binAnnotations file" ) )
	}else{
		binAnnotations <- getBinAnnotations( binSize=binSize, type=experimentType )
	}

	## in case of debug just use inbuilt LGG data for speedup
	if ( debug ){
		data(LGG150)
		readCounts <- LGG150
	}else{
		## provide bamnames because in galaxy everyting is called "dataset_###"
		readCounts <- binReadCounts( binAnnotations, bamfiles=fileList[[ 'all_paths' ]], bamnames=fileList[[ 'all_names' ]] )	
	}

	readCountsFiltered    <- applyFilters( readCounts, residual=TRUE, blacklist=filterBlacklistedBins, mappability=mappabilityCutoff, chromosomes=excludeChrs )
	readCountsFiltered    <- estimateCorrection( readCountsFiltered )
	copyNumbers           <- correctBins( readCountsFiltered )
	copyNumbersNormalized <- normalizeBins( copyNumbers )
	copyNumbersSmooth     <- smoothOutlierBins( copyNumbersNormalized )
	sampleNames           <- readCountsFiltered@phenoData@data$name

	## save objects to output dir
	saveRDS( readCountsFiltered, robjReadCoPath );
	saveRDS( copyNumbersSmooth, robjCopyNrPath );
	exportBins( copyNumbersSmooth, file=igvCopyNrPath, format="igv" )

	## also save objects for galaxy history output if requested
	if ( doOutputCopynumbersIgv ){
		#@ a bit hacky galaxy way to allow an unknown number of output files based on param selection
		#@ see: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
		historyName <- paste(binSize, 'kbp-IGV', sep="")
		igvFile <- paste( newFilePath, "/primary_", outputId, "_", historyName, "_visible_txt", sep="" )
		exportBins( copyNumbersSmooth, file=igvFile, format="igv" )
		catMsg( c("Exported igv file to history for ", binSize, "kbp bin") )
	}

	## proceed with calling if requested
	if ( doSegment ){
		copyNumbersSegmented  <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD )
		copyNumbersSegmented  <- normalizeSegmentedBins( copyNumbersSegmented )
		cgh <- makeCgh( copyNumbersSegmented )
		saveRDS( copyNumbersSegmented, robjSegmntPath );
	}

	## ------------------------
	## create output files
	## ------------------------
	png( noiseImgPath, width=PLOT_HEIGHT, height=PLOT_HEIGHT, res=PLOT_RES );
		par( PAR_SET )
		noisePlot( readCountsFiltered, main=paste( "Noise Plot ", binSize, "kbp", sep=''), col="darkgreen" )
	dev.off()

	binSize <- as.character( binSize ) # to avoid R using it as array index... (*#$^@ you R!)
	binSizeString <- paste( binSize, 'kbp', sep='')

	for (i in 1:length(sampleNames) ){
		
		sample <- sampleNames[i]
		usedReads  <- readCountsFiltered@phenoData@data$used.reads[i]
		catMsg( c("Creating plots for sample: ", sample, " (", binSizeString, ")" ) )	

		type <- 'CopyNumbers'
		img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
		img_file_path <- paste( outputPath, '/', img_file, sep='' )

		## COPYNUMBER PLOT
		png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
			par( PAR_SET )
			plot( copyNumbersSmooth[ ,sample ], main=paste(sample, ": CopyNumbers", sep="") ) 
			mtext( paste( binSizeString, " bins", sep=""), 3 )
			abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
		dev.off()
		
		plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file
		
		if ( doSegment ){
			type <- 'Segmented'
			img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
			img_file_path <- paste( outputPath, '/', img_file, sep='' )
			
			## COPYNUMBER PLOT
			png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
				par( PAR_SET )
				plot( copyNumbersSegmented[ ,sample ], main=paste(sample, ": CopyNumbers and Segments", sep="") )
				mtext( paste( "(", binSizeString, " bins)", sep=""), 3 )
				abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
			dev.off()

			plotted_images[[ paste(binSize, sample, type, sep="_" ) ]] <- img_file

			catMsg( c(" Fusing regions of sample: ", sample) )
			regions[[ sample ]] <- fuseRegions( cgh[, sample] )

			region_count <- nrow( data.frame( regions[[ sample ]] ) )
			catMsg( c( ' sample "', sample, '" has ', region_count, " regions" ) )
			plotted_images[[ paste(binSize, sample, 'region_count', sep="_" ) ]] <- region_count
		}
		
		## add USED read counts
		plotted_images[[ paste(binSize, sample, 'usedReads', sep="_" ) ]] <- usedReads
	}

	if ( doSegment ){
		saveRDS( regions, robjRegionPath )
		plotted_images <- outputRegionsFromList( regions, outputBasename=outputName, outputDir=outputPath, binSize=binSize, storeList=plotted_images )	
	}
}# end bin


## ----- debug -----
#catMsg( "done" )
#q(status=0)
## ---- /debug -----


## ------------------------
## prepare output
## ------------------------
catMsg( "...zipping output")
zip_cmd <- paste( "zip -j", gzipOutputPath, paste(outputPath,'/*',sep='') ) ## -j is for removing dirs from the tree
system( zip_cmd )

## ------------------------
## get filesizes for report
## ------------------------
zippedSize <- paste( round( file.info( gzipOutputPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
endTime <- Sys.time()
timeDiff <- format( round( endTime - startTime, 3 ) )
analysisEnd <- as.character( endTime )

## ------------------------
## creating html output to be linked to from the middle galaxy pane
## ------------------------
sink( file = htmlOutputPath, type = "output" )
		cat( "<html>\n")
		cat( "<head>\n")

			cat( "\t", '<title>QDNAseq Report | ', outputName,'</title>', "\n", sep='' )
			cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )
			cat( "\t<style>\n", sep='')
				## include CSS into html file, makes it more portable
				cat( "\t\t", readLines( CSS_FILE ), sep="\n\t\t" )
				#cat( "\t\th1 {color:red;}", "\n")
			cat( "\n\t</style>\n" )
			
		cat( "\n</head>\n")
		cat( "\n<body>\n")

		cat( "<h1>QDNAseq Report</h1>", "\n")
		
		cat( '<h3 class="qdnaseq">About this analysis</h3>', "\n")
		cat( '<p>This page provides access to all results. To have a local copy of this report just download the <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep='')		
		
		## ------------------------
		## table with general info
		## ------------------------
		cat( '<h3 class="qdnaseq">Settings</h3><p>', "\n")
		cat( '<table class="pure-table pure-table-striped"><tbody>' )
			cat( htmlTableRow( c( "AnalysisName", outputName ) ) )
			cat( htmlTableRow( c( "AnalysisStart", analysisStart ) ) )
			cat( htmlTableRow( c( "AnalysisEnd", analysisEnd ) ) )
			cat( htmlTableRow( c( "AnalysisTime", timeDiff ) ) )
			cat( htmlTableRow( c( "BinSizes (kbp)", paste(binSizes,collapse=", ") ) ) )
			cat( htmlTableRow( c( "R info", rVersion ) ) )
			cat( htmlTableRow( c( "QDNAseq info", qdnaseqVersion ) ) )
			
			sampleStrings <- c()
			for ( galaxyName in fileList[[ 'all_files' ]] ){
				sampleName <- fileList[[ galaxyName ]]
				sampleStrings <- c( sampleStrings, paste( galaxyName, ' (', sampleName, ')', sep='' ) )
			}
			cat( htmlTableRow( c( "InputBams", paste( sampleStrings, collapse=", ") ) ) )

		cat( "</tbody></table></p>", "\n")
		
		## ------------------------
		## list with links to all output files
		## ------------------------
		cat( '<h3 class="qdnaseq">Output files</h3><p>', "\n")
		cat( '<p>This table contains output files that can be used for local downstream analysis with the bioconductor QDNAseq package. For each bin-size / data-level there is a R data structure file with data of all samples. See ', htmlLink( WEB_LINK, 'the bioconductor QDNAseq documentation' ), ' for more information on how to work with these files</p>', "\n", sep='')
		cat( '<table class="pure-table pure-table-striped">', "\n" )
		cat( '<thead><th>Type</th>', as.vector( mapply( paste, "<th>", binSizes, "kbp</th>", sep="" ) ),'</thead>', "\n" )
		cat( "<tbody>", "\n")
			files <- list()
			fileTypes <- c( 'ReadCounts.rds', 'CopyNumbers.rds' )
			if ( doSegment ){ fileTypes <- c( fileTypes, 'CopyNumbersSegmented.rds') }

			for ( fileType in fileTypes ){
				fileNames <- mapply( paste, binSizes, paste( 'kbp_QDNAseq', fileType, sep=''), sep='')
				fileLinks <- mapply( htmlLink, fileNames, paste( binSizes, "kbp", sep="" ) )
				cat( htmlTableRow( c( fileType, fileLinks ) ) )	
			}
		cat( "\n</tbody></table></p>", "\n")

		## ------------------------
		## table with links to files	
		## ------------------------
		ratio <- PLOT_WIDTH / PLOT_HEIGHT
		width <- 960; height <- width / ratio ## bigger img
		width_t <- 100; height_t <- 40 ## thumb img

		cat( '<h3 class="qdnaseq">Results: overview</h3><p>', "\n")
		cat( '<p>This table contains the visual results of the copy number aberration analysis. You can click on an image to jump to the larger version. If segmentation was performed as well the number of segments is shown and a file with genomic regions can be downloaded (just remember to inspect the results carefully as this is a more exprimental step).</p>', "\n", sep='')
		plots_html <- ''

		colspan <- 1
		binHeader <- "<th>Image</th>"
		if ( doSegment ){ # extra column with segment info
			colspan <- 2 
			binHeader <- "<th>Image</th><th>Segments</th>"
		} 
		cat( '<table class="pure-table pure-table-striped">', "\n" )
		cat( '<thead><tr><th></th><th></th>', as.vector( mapply( paste, "<th colspan=\"", colspan,"\">", binSizes, "kbp</th>", sep="" ) ), '</tr></thead>' )
		cat( '<thead><tr><th>Sample / File</th><th>Reads</th>', rep( binHeader, length(binSizes) ), '</tr></thead>' )
		cat( '<tbody>' )

			for ( bam_file in bamsNames ){
				
				usedReads <- plotted_images[[ paste(binSize, bam_file, 'usedReads', sep="_" ) ]]
				usedReads <- format( as.integer(usedReads), digits=4, decimal.mark=".", big.mark="," )
				htmlRow <- paste( '<tr><td>', bam_file, '</td><td>', usedReads, '</td>', sep='' )

				for ( binSize in binSizes ){
					
					## add thumbnails to table with links to anchors on html page
					copy_img <- plotted_images[[ paste(binSize, bam_file, 'CopyNumbers', sep="_" ) ]]
					html_copy_thumb <- htmlLink( path=paste('#', copy_img, sep=''), paste('<img src="',copy_img,'" alt="', bam_file, '" width="', width_t, '" height="', height_t, '">', sep='') )
					html_copy_img <- htmlLink( path=copy_img, paste('<img id="', copy_img,'" src="',copy_img,'" alt="',bam_file, '" width="', width, '" height="', height, '">', sep='') )
					html_segm_img <- ''
					html_bedGraph <- ''
					region_count <- ''
					htmlRow <- paste( htmlRow, '<td>', html_copy_thumb, '</td>' )

					if ( doSegment ){
						segm_img <- plotted_images[[ paste(binSize, bam_file, 'Segmented', sep="_" ) ]]
						region_count <- plotted_images[[ paste(binSize, bam_file, 'region_count', sep="_" ) ]]

						html_bedGraph <- htmlLink( path=plotted_images[[ paste(binSize, bam_file, 'bedgraph', sep="_" ) ]], 'bedGraph' )
						html_segm_img <- htmlLink( path=segm_img, paste('<img id="', segm_img,'" src="', segm_img,'" alt="', bam_file, '" width="', width, '" height="', height,'">', sep='') )
						htmlRow <- paste( htmlRow, '<td>', region_count, ' (', html_bedGraph, ')</td>', sep="" )
					}
					plots_html <- paste( plots_html, html_copy_img, "\n", html_segm_img, "\n<br \\>\n", sep='' )	
				}
				plots_html <- paste( plots_html, "\n<hr \\>\n", sep='' )
				## add info to overview table, including small thumbnails
				htmlRow <- paste( htmlRow, '</tr>', sep='' )
				cat( htmlRow, "\n" )				
			}
		cat( "</tbody></table></p>", "\n")
		
		## ------------------------
		## section with various output shown
		## ------------------------
		cat( '<h3 class="qdnaseq">Results: Sample plots</h3><p>', "\n")
		## now include (large) images in html page
		cat( plots_html, "\n")
		cat( "\n</p></body>\n")
		cat( "\n</html>\n")
sink()

## ------------------------
## creating main html output for galaxy history
## ------------------------
if ( inGalaxy ){ # dont create when running outside Galaxy
	sink( file = outputHtml, type = "output" )
			
		cat( "<head>", "\n")
			cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )

			cat( "<style>", "\n")
				## include CSS directly into html file
				cat( paste( "\t", '/* the css here originates from ', CSS_FILE,' */', "\n") )
				cat( paste( "\t", readLines( CSS_FILE, n = -1)), sep="\n" )
			cat( "</style>", "\n")
		cat( "</head>", "\n")

		cat( '<h1>QDNAseq Results (', outputName,')</h1>', "\n", sep="")
		cat( '<p>Explore <a href="', htmlOutputName, '" class="button">the results</a> directly within galaxy</p>', "\n", sep="")
		cat( '<p>Or download a <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep="" )

	sink()
}

## ------------------------
## create final zip and quit with status 0 to tell galaxy all was fine
## ------------------------
catMsg( "zipping all output")
system( paste( "zip -j ", gzipOutputPath, paste(outputPath,'/', htmlOutputName, sep='') ) )
catMsg( "done" )
q(status=0)