diff createHTML.sh @ 6:42076db43d42 draft

Fixed auto resizing plus various other minor bugs

--- a/createHTML.sh	Tue Oct 07 08:49:14 2014 -0400
+++ b/createHTML.sh	Mon Nov 16 08:56:22 2015 -0500
@@ -1,6 +1,9 @@
+gbcount=0
+
 ##
 ## Create Cover Page
 ##
+#<a href=\"$zipireport\">  Click here to download a copy of this iReport </a> <br/><br/>
 function makeIntroPage  ( ){
 	echo "Creating Intro Page"
 	title="$1"
@@ -20,9 +23,8 @@
 		<b><font size=\"15\"> iReport: ${title} </font></b><br/>
 		<br/>
 		<br/>
-		<a href=\"$link\">  Click here to view report	</a> <br/><br/>
+		<a href=\"$link\">  Click image to view report	</a> <br/><br/>
 		<a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>		
-		<a href=\"$zipireport\">  Click here to download a copy of this iReport </a> <br/><br/>
 		</center>
 	</body>
 </html>" > $htmlout
@@ -30,14 +32,86 @@
 }
 
 ##
+## Decompress archive fiels
+##  -> will detect archive formats: zip, tar, gzip, tar.gz, bzip2
+##  -> input: path to archive
+##  -> files will be located in ${galaxypath}/archive_${fname}/
+##
+function decompressArchive (){
+	archive=$1
+	
+	fname=`basename ${archive}`
+	fname=${fname%.dat}
+	ftype=`file $archive`
+	
+	if [[ ! -d ${galaxypath}/archive_${fname}/ ]]
+	then
+		mkdir ${galaxypath}/archive_${fname}/
+		
+		#echo "archive type: `file $archive`"
+		# decompress archive
+		if [[ $ftype == *Zip* ]]
+		then
+		#echo "detected zip file"
+			cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
+			wd=`pwd`
+			cd ${galaxypath}/archive_${fname}/
+			unzip -q ${fname}.zip
+			rm ${fname}.zip
+			cd $wd
+		fi
+		if [[ $ftype == *tar* ]]
+		then
+			cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
+			wd=`pwd`
+			cd ${galaxypath}/archive_${fname}/
+			tar xf ${fname}.tar
+			rm ${fname}.tar
+			cd $wd
+		fi
+		if [[ $ftype == *gzip* ]]
+		then
+			cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
+			gunzip ${galaxypath}/archive_${fname}/${fname}.gz
+			#ls ${galaxypath}/archive_${fname}/
+			
+			# check for tar.gz
+			ftype=`file ${galaxypath}/archive_${fname}/${fname}`
+			if [[ $ftype == *tar* ]]
+			then
+				# turns out it was tar.gz
+				rm -Rf ${galaxypath}/archive_${fname}/*
+				ls ${galaxypath}/archive_${fname}/
+				cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
+				
+				wd=`pwd`
+				cd ${galaxypath}/archive_${fname}/
+				tar xzf ${fname}.tar.gz 
+				cd $wd
+			fi
+			wait
+			rm -f ${galaxypath}/archive_${fname}/*.tar
+			rm -f ${galaxypath}/archive_${fname}/*.tar.gz
+		fi
+		if [[ $ftype == *bzip2* ]]
+		then
+			cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
+			gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
+		fi
+	fi
+}
+
+##
 ## Create HTML content for the tabs specified by user
 ##
 function makeTabContent ( ){
 	tab=$1			# name of current tab
 	itemslist=$2	# list of all items
+	tracklist=$3	# genome browser tracks info
 	contentline=""  # HTML code for tab
 	imgcount=0		# keep track of the number of images on the current tab
-	
+	iframename=`head -n 1 < /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 8 | head -n 1`
+	#iframename="test"
 	for item in $itemslist
 	do
 		## Parse items lists
@@ -63,6 +137,12 @@
 					text=${text//==space==/ }
 					text=${text//==colon==/:}
 					text=${text//==comma==/,}
+					
+					text=${text//==braceopen==/(}
+					text=${text//==braceclose==/)}
+					text=${text//==cbraceopen==/{}
+					text=${text//==cbraceclose==/&#125;}
+					
 					text=${text//==slash==/\/}
 					text=${text//==lt==/<}
 					text=${text//==gt==/>}
@@ -78,8 +158,8 @@
 					text=${text//\&r/\\n}
 					text=${text//\&n/\\n}
 					text=${text//\&c/:}
-					
-					
+
+						
 					## convert markdown in textfield to html
 					echo -e "$text" > mytext.md
 					
@@ -90,9 +170,8 @@
 						
 					else
 						# pandoc exists 
-						echo "pandoc exists"
-						pandoc -o mytext.html mytext.md
-						pandoc -o standalone.html -s mytext.md
+						pandoc -f markdown -o mytext.html mytext.md
+						pandoc -f markdown -o standalone.html -s mytext.md
 						
 						#get css generated by pandoc and add as scoped attribute (HTML5)
 						pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
@@ -148,6 +227,10 @@
 					text=${text//==backtick==/&#96;}
 					text=${text//==dollar==/$}
 					text=${text//==bar==/|}
+					text=${text//==braceopen==/(}
+					text=${text//==braceclose==/)}
+					text=${text//==cbraceopen==/{}
+					text=${text//==cbraceclose==/&#125;}
 					contentline="${contentline}\n${text}\n"
 				fi
 				
@@ -208,6 +291,7 @@
 				zoomlevel=${myarr[4]}
 				zoomenable=${myarr[5]}
 				align=${myarr[6]}
+				typestring=""
 				#####echo "zoomenable:${zoomenable}, align:${align}"
 				if [[ $ftype == *JPEG* ]]
 				then
@@ -221,6 +305,11 @@
 				then
 					suffix=".png"
 				fi
+				if [[ $ftype == *TIFF* ]]
+				then
+					suffix=".tiff"
+					typestring="type=\"image/tiff\""
+				fi
 				
 				image=`basename ${myarr[2]}`
 				image=${image%.dat}
@@ -248,8 +337,8 @@
 				fi
 				
 				if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
-				then
-					contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
+				then                                    
+					contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"                                    
 				else				
 					contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
 				fi
@@ -261,6 +350,7 @@
 			##	
 			if [ ${myarr[1]} == "table" ]
 			then
+				
 				maxlines=50000
 				tsvfile_orig=${myarr[2]}
 				tsvfile="tablehead.tsv"
@@ -268,6 +358,9 @@
 				fname=${fname%.*}
 				fancy=${myarr[4]}
 				makelinks=${myarr[5]}
+				#iframeid="iframe$giframecount"
+				iframeid="iframe-$iframename"
+				
 				#echo "\nmakelinks: $makelinks fancy: $fancy <br>"
 				
 				#TODO client side database for large files. For now only display first section of file and add download link
@@ -291,13 +384,25 @@
 				then
 					col=${myarr[6]}
 					prefix=${myarr[7]}
-					suffix=${myarr[8]}					
+					suffix=${myarr[8]}
+					urlitems=${myarr[9]}
+					minw=${myarr[10]}
+					minh=${myarr[11]}
 					suffix=${suffix/emptycol/}
 					suffix=${suffix/==quote==/&}
 					prefix=${prefix/emptycol/}
 					prefix=${prefix/==quote==/&}
 					prefix=${prefix/==colon==/:}
-					#echo "prefix: $prefix"
+					
+					# unpack archive of files to link to if present
+					if [[ ${urlitems} != None ]]
+					then
+						oldfname=$fname
+						decompressArchive ${urlitems}
+						prefix=archive_${fname}/${prefix}
+						fname=$oldfname
+					fi
+					
 					
 					#edit the table to include links
 					awk 'BEGIN{
@@ -305,32 +410,37 @@
 						OFS="\t"
 						url="'"$prefix"'"
 						url2="'"$suffix"'"
+						iframeid="'"$iframeid"'"
 						prefix="<a href=\42"
-						suffix="\42>"
+						suffix="\42 onclick=\42resizeIframe("iframeid")\42>"
 						col="'"$col"'"
 						end="</a>"
 					}{
 						if(FNR==1)
 							print $0
-						else{
+					else{
 							$col=prefix""url""$col""url2""suffix""$col""end
 							print $0
 						}
 					}END{}' ${tsvfile} > ${tsvfile}2
-
+				
 				else
+					minw=${myarr[6]}
+					minh=${myarr[7]}
 					cp ${tsvfile} ${tsvfile}2
 				fi
 				
+				#iframecount=$[$iframecount+1]
+				
 				if [ $fancy == "Y" ]
 				then
 					perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
-					contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"min-height: 525px; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
-					iframecount=$[$iframecount+1]
+					contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 350px; min-height: ${minh}px !important; overflow-y: hidden; overflow-x: scroll\" onClick=resizeIframe(\"$iframeid\")></iframe>"
+					
 				else
 					perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
-					contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
-					iframecount=$[$iframecount+1]
+					contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; min-height: ${minh}px !important; max-width: 100%; vertical-align: top;\" onClick=resizeIframe(\"$iframeid\") ></iframe>"
+					
 				fi
 				
 				if [[ $numlines -gt ${maxlines} ]]
@@ -373,7 +483,29 @@
 				htmlname="${fname}.html"
 				cp ${htmlfile} "${galaxypath}/${htmlname}"
 				
-				contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
+				apiid=${myarr[5]}
+				isireport=${myarr[6]}
+				localhost=${myarr[7]}
+				proxy=${myarr[8]}
+				localhost=${localhost//==colon==/:}
+				localhost=${localhost//==fslash==/\/}
+				if [[ ${isireport} == "Y" ]]
+				then
+					#cp ${localhost}/datasets/${apiid}/* "${galaxypath}/tst"
+					htmlname="/${proxy}/datasets/${apiid}/display/"
+				fi
+				
+				contentline="${contentline}\n<iframe  class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
+			fi
+			
+			
+			if [[ ${myarr[1]} == "htmlpage" ]]
+			then
+				url=${myarr[2]}
+				url=${url//==colon==/:}
+				url=${url//==fslash==//}
+				height=${myarr[4]}
+				contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
 			fi
 			
 			##
@@ -383,12 +515,280 @@
 			then
 				url=${myarr[2]}
 				linktext=${myarr[4]}				
-				url=${url/==colon==/:}
-				url=${url/==quote==/&}
+				
+				echo -n "$url" > tmpfileb64
+				url=`base64 -d tmpfileb64`
 				
+				echo -n "$linktext" > tmpfileb64
+				linktext=`base64 -d tmpfileb64`
+				
+				if [[ -z $linktext ]]
+				then
+					linktext=$url
+				fi
 				contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
 			fi
 			
+
+			##
+			##  Genome Browser
+			##	
+			if [ ${myarr[1]} == "genomebrowser" ]
+			then
+				
+				# parse inputs
+				
+				apiid=${myarr[4]}
+				servername=${myarr[5]}
+				buildver=${myarr[2]}
+				
+				
+				region=${myarr[6]}
+				
+				
+				echo -n "$region" > tmpfileb64
+				region=`base64 -d tmpfileb64`
+				
+				
+				initialchrom=${region%:*}
+				initialrange=${region#*:}
+				
+				initialstart=${initialrange%-*}
+				initialend=${initialrange#*-}
+				
+				
+				#TODO 
+				ftype="vcf"
+				
+				servername=${servername/==colon==/:}
+				
+				## parse and prepare all tracks
+				gbcount=$[$gbcount+1]
+				gbfilelist=${tracklist}
+				userTracks=""
+				#IFS=',' read -a gbfilearray <<< ${gbfilelist}
+				gbfilearray=(${gbfilelist//,/ })
+				for gbfile in "${gbfilearray[@]}"
+				do
+					# gbfile is in format "browsernum:file"
+					#IFS=':' read -a gbfileinfo <<< ${gbfile}
+					gbfileinfo=(${gbfile//:/ })
+					if [[ ${gbfileinfo[0]} == $gbcount ]]
+					then
+					
+						ftype=${gbfileinfo[3]}
+						
+						gbfilename=${gbfileinfo[1]}
+						gbfilelabel=${gbfileinfo[2]}
+						gbfilelabel=${gbfilelabel//==space==/ }
+						gbfilelabel=${gbfilelabel//==bopen==/(}
+						gbfilelabel=${gbfilelabel//==bclose==/)}
+						fname=`basename ${gbfilename}`	
+						fname=${fname%.dat}
+						
+						if [[ $ftype == "vcftabix" ]]
+						then
+							newgbfilename="${fname}.vcf"
+							
+							
+							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
+							bgzip "${galaxypath}/${newgbfilename}"
+							tabix -f -p vcf "${galaxypath}/${newgbfilename}.gz"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								uri:                  '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
+								tier_type:            'tabix',
+								payload:              'vcf'}
+							"
+						fi
+						
+						if [[ $ftype == "vcfmemstore" ]]
+						then
+							newgbfilename="${fname}.vcf"
+							
+							
+							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
+							#bgzip "${galaxypath}/${newgbfilename}"
+							#tabix -p vcf "${galaxypath}/${newgbfilename}.gz"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								uri:                  '${servername}/datasets/${apiid}/display/${newgbfilename}',
+								tier_type:            'memstore',
+								payload:              'vcf'}
+							"
+						fi
+						
+						if [[ $ftype == "bam" ]]
+						then
+							newgbfilename="${fname}.bam"
+							
+							# link to bam instead of copying
+							ln -s ${gbfilename} "${galaxypath}/${newgbfilename}"
+							samtools index "${galaxypath}/${newgbfilename}"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								 bamURI:                  '${servername}/datasets/${apiid}/display/${newgbfilename}'}
+							"
+						
+						fi
+						
+						if [[ $ftype == "bigbed" ]]
+						then
+							newgbfilename="${fname}.bigbed"
+							
+							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
+							#bgzip "${galaxypath}/${newgbfilename}"
+							#tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								bwgURI:                  '${servername}/datasets/${apiid}/display/${newgbfilename}'}
+							"
+						
+						fi
+						
+						if [[ $ftype == "bedtabix" ]]
+						then
+							newgbfilename="${fname}.bed"
+							
+							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
+							bgzip "${galaxypath}/${newgbfilename}"
+							tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								uri:                  '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
+								tier_type:            'tabix',
+								payload:              'bed'}
+							"
+						
+						fi
+						
+						if [[ $ftype == "bedmemstore" ]]
+						then
+							newgbfilename="${fname}.bed"
+							
+							cp ${gbfilename} "${galaxypath}/${newgbfilename}"
+							#bgzip "${galaxypath}/${newgbfilename}"
+							#tabix -p bed "${galaxypath}/${newgbfilename}.gz"
+							
+							userTracks="${userTracks},
+								{name:                 '${gbfilelabel}',
+								uri:                  '${servername}/datasets/${apiid}/display/${newgbfilename}',
+								tier_type:            'memstore',
+								payload:              'bed'}
+							"
+						
+						fi
+					fi
+				done
+				
+				
+				
+				if [ ${buildver} == "hg18" ]
+				then
+					coordSystem="coordSystem: {
+							speciesName: 'Human',
+							taxon: 9606,
+							auth: 'NCBI',
+							version: '36',
+							ucscName: 'hg18'
+							},"
+
+					chains="chains: {
+								hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
+									{
+										speciesName: 'Human',
+										taxon: 9606,
+										auth: 'GRCh',
+										version: 37
+									})
+								},"
+
+					genesTrack="{name:                'Genes',
+								desc:                 'Gene structures from Ensembl 54',
+								uri:                  'https://www.biodalliance.org/das/hsa_54_36p/',
+								collapseSuperGroups:  true,
+								provides_karyotype:   true,
+								provides_search:      true,
+								provides_entrypoints: true,
+								maxbins:              false}, "
+
+					repeatsTrack="{name:                'Repeats',
+									desc:                 'Repeat annotation from Ensembl 59', 
+									bwgURI:               'https://www.biodalliance.org/datasets/repeats.bb',
+									stylesheet_uri:       'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}"
+
+
+				# default is hg19
+				else
+					coordSystem="coordSystem: {
+							speciesName: 'Human',
+							taxon: 9606,
+							auth: 'NCBI',
+							version: '37',
+							ucscName: 'hg19'
+							},"
+
+					chains=""
+
+					genesTrack="{name:                'Genes',
+								desc:                 'Gene structures from GENCODE 19',
+								bwgURI:               'https://www.biodalliance.org/datasets/gencode.bb',
+								stylesheet_uri:       'https://www.biodalliance.org/stylesheets/gencode.xml',
+								collapseSuperGroups:   true,
+								trixURI:              'https://www.biodalliance.org/datasets/geneIndex.ix'},"
+
+					repeatsTrack="{name:                'Repeats',
+									desc:                 'Repeat annotation from Ensembl 59', 
+									bwgURI:               'https://www.biodalliance.org/datasets/repeats.bb',
+									stylesheet_uri:       'https://www.biodalliance.org/stylesheets/bb-repeats.xml'},"
+									
+				fi
+				
+				contentline="${contentline}
+<script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script>
+<script language=\"javascript\">
+  new Browser({
+    chr:          '$initialchrom',
+    viewStart:    $initialstart,
+    viewEnd:      $initialend,
+    cookieKey:    'human',
+    pageName:     'svgHolder${gbcount}',
+    ${coordSystem}
+
+	${chains}
+    sources:     [{name:                 'Genome',
+                   twoBitURI:            'https://www.biodalliance.org/datasets/${buildver}.2bit',
+                   tier_type:            'sequence'},
+                  ${genesTrack},
+                  ${repeatsTrack},
+                  {name:                 'Conservation',
+                   desc:                 'Conservation', 
+                   bwgURI:               'https://www.biodalliance.org/datasets/phastCons46way.bw',
+                   noDownsample:          true} 
+                  ${userTracks}
+                 ],
+
+
+
+	
+    browserLinks: {
+      Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
+      UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}',
+      Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}'
+    }
+
+  });
+</script>
+
+<div id=\"svgHolder${gbcount}\"></div>
+"
+			fi
+
 			##
 			##  Link to Dataset
 			##	
@@ -400,6 +800,10 @@
 				linkfilename=`basename ${linkfile}`
 				linktext=${myarr[6]}
 				
+				localhost=${myarr[7]}
+				proxy=${myarr[8]}
+				localhost=${localhost//==colon==/:}
+				localhost=${localhost//==fslash==/\/}
 				
 				#check for some basic filetypes
 				ftype=`file $linkfile`
@@ -427,7 +831,7 @@
 				
 				if [[ ${isireport} == "Y" ]]
 				then					
-					linkfilename="/datasets/${apiid}/display/"
+					linkfilename="/${proxy}/datasets/${apiid}/display/"
 				else
 					cp ${linkfile} "${galaxypath}/${linkfilename}"
 				fi
@@ -439,67 +843,10 @@
 			##  Links to Archive Contents
 			##	
 			if [[ ${myarr[1]} == "links" ]]
-			then
-				#echo "making links:"
+			then			
 				archive=${myarr[2]}
-				fname=`basename ${archive}`
-				fname=${fname%.dat}
-				ftype=`file $archive`
-				mkdir ${galaxypath}/archive_${fname}/
-				
-				#echo "archive type: `file $archive`"
-				# decompress archive
-				if [[ $ftype == *Zip* ]]
-				then
-					#echo "detected zip file"
-					cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
-					wd=`pwd`
-					cd ${galaxypath}/archive_${fname}/
-					unzip -q ${fname}.zip
-					rm ${fname}.zip
-					cd $wd
-				fi
-				if [[ $ftype == *tar* ]]
-				then
-					cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
-					wd=`pwd`
-					cd ${galaxypath}/archive_${fname}/
-					tar xf ${fname}.tar
-					rm ${fname}.tar
-					cd $wd
-				fi
-				if [[ $ftype == *gzip* ]]
-				then
-					cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
-					gunzip ${galaxypath}/archive_${fname}/${fname}.gz
-					#ls ${galaxypath}/archive_${fname}/
-					
-					# check for tar.gz
-					ftype=`file ${galaxypath}/archive_${fname}/${fname}`
-					if [[ $ftype == *tar* ]]
-					then
-						# turns out it was tar.gz
-						rm -Rf ${galaxypath}/archive_${fname}/*
-						ls ${galaxypath}/archive_${fname}/
-						cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
-						
-						wd=`pwd`
-						cd ${galaxypath}/archive_${fname}/
-						tar xzf ${fname}.tar.gz 
-						cd $wd
-					fi
-					wait
-					rm -f ${galaxypath}/archive_${fname}/*.tar
-					rm -f ${galaxypath}/archive_${fname}/*.tar.gz
-				fi
-				if [[ $ftype == *bzip2* ]]
-				then
-					cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
-					gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
-				fi
-				
-				
-				
+				decompressArchive $archive
+
 				# add links to webpage
 				# separate line for each folder, files within folder on same line
 				for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
@@ -540,36 +887,55 @@
 	done
 	
 	echo "${contentline}"
+	
+	
 }
 
 ##
 ## Create HTML content for iReport
 ##
 createMainPage (){
+        #export IFRAMECNT=1
 	page=$1
 	tabtitles=$2	# comma-separated list of tab titles
 	tabitems=$3		# colon-sparated list of tabs specifications
-	iframecount=1	# keep track of number of iFrames so that they can be referenced by ID
+	#giframecount=1	# keep track of number of iFrames so that they can be referenced by ID
 	minwidth=$4		# width of page
+	gbtracks=$5		# genome browser track information
 	
-	echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles"
+	echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
 	# create correct number of tabs
 	count=0
 	
+	tabtitles=${tabtitles/,/}
 	tabtitles=${tabtitles//,/ }
-	tabtitles=${tabtitles//==colon==/:}
+	echo $tabtitles
+	
+	tabcount=0
+	for tabt in $tabtitles
+	do
+		echo -n $tabt > tmpfileb64
+		thistabtitle=`base64 -d tmpfileb64`
+		newtabtitles+=" $thistabtitle"
+		tabcount=$[tabcount+1]
+	done
+	
+	echo $newtabtitles
+	
 	tabslist="<ul>\n"
 	mytabs=""
 	
-	for title in $tabtitles
+	for title in $newtabtitles
 	do
 		# Create list of tabs		
 		count=$[count+1]
-		title2=${title//_s_/ }
+		title2=${title//==space==/ }
+		title2=${title2//==dollar==/$}
+		title2=${title2//==colon==/}
 		tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
 		
 		# Create tabs with content
-		tabcontent=$(makeTabContent $title "$tabitems")
+		tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks")
 		mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
 		mytabs="${mytabs}${tabcontent}"
 		mytabs="${mytabs}\n</div>\n"
@@ -599,4 +965,4 @@
   </div>
  </body>
 </html>" > $page
-}
\ No newline at end of file
+}