ireport: createHTML.sh annotate

annotate createHTML.sh @ 8:86219e4aa239 draft

Uploaded

author	saskia-hiltemann
date	Mon, 28 Aug 2017 10:23:21 -0400
parents	42076db43d42
children

rev	line source
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	1 gbcount=0
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	2
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	3 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	4 ## Create Cover Page
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	5 ##
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	6 #<a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	7 function makeIntroPage ( ){
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	8 echo "Creating Intro Page"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	9 title="$1"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	10 coverimage=$2
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	11 link=$3
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	12 htmlout=$4
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	13 zipireport=$5
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	14
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	15 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	16 <html>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	17 <head>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	18 </head>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	19 <body>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	20 <br/>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	21 <br/>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	22 <center>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	23 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	24 <br/>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	25 <br/>
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	26 <a href=\"$link\"> Click image to view report </a> <br/><br/>
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	27 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	28 </center>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	29 </body>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	30 </html>" > $htmlout
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	31
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	32 }
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	33
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	34 ##
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	35 ## Decompress archive fiels
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	36 ## -> will detect archive formats: zip, tar, gzip, tar.gz, bzip2
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	37 ## -> input: path to archive
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	38 ## -> files will be located in ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	39 ##
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	40 function decompressArchive (){
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	41 archive=$1
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	42
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	43 fname=`basename ${archive}`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	44 fname=${fname%.dat}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	45 ftype=`file $archive`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	46
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	47 if [[ ! -d ${galaxypath}/archive_${fname}/ ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	48 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	49 mkdir ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	50
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	51 #echo "archive type: `file $archive`"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	52 # decompress archive
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	53 if [[ $ftype == Zip ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	54 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	55 #echo "detected zip file"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	56 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	57 wd=`pwd`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	58 cd ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	59 unzip -q ${fname}.zip
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	60 rm ${fname}.zip
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	61 cd $wd
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	62 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	63 if [[ $ftype == tar ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	64 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	65 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	66 wd=`pwd`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	67 cd ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	68 tar xf ${fname}.tar
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	69 rm ${fname}.tar
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	70 cd $wd
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	71 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	72 if [[ $ftype == gzip ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	73 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	74 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	75 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	76 #ls ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	77
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	78 # check for tar.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	79 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	80 if [[ $ftype == tar ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	81 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	82 # turns out it was tar.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	83 rm -Rf ${galaxypath}/archive_${fname}/*
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	84 ls ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	85 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	86
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	87 wd=`pwd`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	88 cd ${galaxypath}/archive_${fname}/
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	89 tar xzf ${fname}.tar.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	90 cd $wd
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	91 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	92 wait
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	93 rm -f ${galaxypath}/archive_${fname}/*.tar
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	94 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	95 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	96 if [[ $ftype == bzip2 ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	97 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	98 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	99 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	100 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	101 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	102 }
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	103
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	104 ##
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	105 ## Create HTML content for the tabs specified by user
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	106 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	107 function makeTabContent ( ){
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	108 tab=$1 # name of current tab
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	109 itemslist=$2 # list of all items
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	110 tracklist=$3 # genome browser tracks info
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	111 contentline="" # HTML code for tab
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	112 imgcount=0 # keep track of the number of images on the current tab
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	113 iframename=`head -n 1 < /dev/urandom \| tr -dc 'a-zA-Z0-9' \| fold -w 8 \| head -n 1`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	114 #iframename="test"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	115 for item in $itemslist
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	116 do
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	117 ## Parse items lists
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	118 item=${item/::/:emptycol:}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	119 declare -a myarr=(`echo $item \|sed 's/:/ /g'`)
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	120
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	121 ## Create the tab contents HTML code
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	122 if [ ${myarr[0]} == $tab ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	123 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	124
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	125 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	126 ## Text Field
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	127 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	128 if [ ${myarr[1]} == "text" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	129 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	130 text=${myarr[2]}
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	131 md=${myarr[4]}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	132
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	133 # if markdown, convert to html
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	134 if [ $md == "Y" ]
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	135 then
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	136 ## resubstitute sanitized charachters
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	137 text=${text//==space==/ }
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	138 text=${text//==colon==/:}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	139 text=${text//==comma==/,}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	140
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	141 text=${text//==braceopen==/(}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	142 text=${text//==braceclose==/)}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	143 text=${text//==cbraceopen==/{}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	144 text=${text//==cbraceclose==/}}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	145
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	146 text=${text//==slash==/\/}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	147 text=${text//==lt==/<}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	148 text=${text//==gt==/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	149 text=${text//==apos==/\'}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	150 text=${text//==quote==/\"}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	151 text=${text//==backtick==/\`}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	152 text=${text//==dollar==/$}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	153 text=${text//==bar==/\|}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	154 text=${text//&&/&}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	155 text=${text//\\n/\\n}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	156 text=${text//\\t/\\t}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	157 text=${text//\&r\&n/\\n}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	158 text=${text//\&r/\\n}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	159 text=${text//\&n/\\n}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	160 text=${text//\&c/:}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	161
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	162
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	163 ## convert markdown in textfield to html
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	164 echo -e "$text" > mytext.md
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	165
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	166 if [ -z `type -p pandoc` ]
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	167 then
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	168 # pandoc missing
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	169 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	170
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	171 else
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	172 # pandoc exists
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	173 pandoc -f markdown -o mytext.html mytext.md
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	174 pandoc -f markdown -o standalone.html -s mytext.md
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	175
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	176 #get css generated by pandoc and add as scoped attribute (HTML5)
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	177 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	178 fi
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	179
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	180 markdowntext=$(cat mytext.html)
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	181 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	182
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	183 else # If not markdown, print verbatim (with exception of few html tags)
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	184
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	185 ## allow some html formatting tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	186 text=${text//==lt==strong==gt==/<strong>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	187 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	188 text=${text//==lt==em==gt==/<em>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	189 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	190
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	191 text=${text//==lt==b==gt==/<strong>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	192 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	193 text=${text//==lt==i==gt==/<em>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	194 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	195
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	196 text=${text//==lt==br==gt==/<br\/>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	197 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	198 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	199 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	200 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	201 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	202 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	203 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	204 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	205 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	206 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	207 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	208 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	209 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	210
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	211 ## display everything else verbatim
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	212 text=${text//==space==/ }
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	213 text=${text//==colon==/:}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	214 text=${text//==comma==/,}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	215 text=${text//==slash==/\/}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	216 text=${text//==lt==/<}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	217 text=${text//==gt==/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	218 text=${text//==apos==/'}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	219 text=${text//==quote==/"}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	220 text=${text//&&/&}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	221 text=${text//\\n/<br/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	222 text=${text//\\t/&emsp;}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	223 text=${text//\&r\&n/<br/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	224 text=${text//\&r/<br/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	225 text=${text//\&n/<br/>}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	226 text=${text//\&c/:}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	227 text=${text//==backtick==/`}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	228 text=${text//==dollar==/$}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	229 text=${text//==bar==/\|}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	230 text=${text//==braceopen==/(}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	231 text=${text//==braceclose==/)}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	232 text=${text//==cbraceopen==/{}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	233 text=${text//==cbraceclose==/}}
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	234 contentline="${contentline}\n${text}\n"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	235 fi
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	236
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	237
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	238 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	239
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	240 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	241 ## Text File
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	242 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	243 if [ ${myarr[1]} == "textfile" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	244 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	245 tfile=${myarr[2]}
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	246 md=${myarr[4]}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	247 fname=`basename ${tfile}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	248 fname=${fname%.*}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	249 fname="${fname}.txt"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	250 cp ${tfile} "${galaxypath}/${fname}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	251
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	252 #estimate height for iframe based on number oflines in the file
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	253 numlines=`wc -l ${tfile} \| cut -d" " -f1`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	254 minheight=$[$numlines*17]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	255
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	256 # if markdown, convert to html
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	257 if [ $md == "Y" ]
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	258 then
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	259
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	260 if [ -z `type -p pandoc` ]
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	261 then
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	262 # pandoc missing
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	263 ${repositorypath}/Markdown/markdown2.py ${tfile} > mytext.html
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	264
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	265 else
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	266 # pandoc exists
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	267 pandoc -o mytext.html ${tfile}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	268 pandoc -o standalone.html -s ${tfile}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	269
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	270 # get css generated by pandoc and add as scoped attribute (HTML5)
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	271 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	272
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	273 fi
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	274
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	275 markdowntext=$(cat mytext.html)
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	276 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	277 else
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	278 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>\n"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	279 fi
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	280 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	281
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	282 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	283 ## Image
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	284 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	285 if [ ${myarr[1]} == "image" ]
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	286
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	287 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	288 imgcount=$[$imgcount+1]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	289 #restore file suffix for html
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	290 ftype=`file ${myarr[2]}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	291 zoomlevel=${myarr[4]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	292 zoomenable=${myarr[5]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	293 align=${myarr[6]}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	294 typestring=""
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	295 #####echo "zoomenable:${zoomenable}, align:${align}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	296 if [[ $ftype == JPEG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	297 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	298 suffix=".jpg"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	299 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	300 if [[ $ftype == SVG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	301 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	302 suffix=".svg"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	303 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	304 if [[ $ftype == PNG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	305 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	306 suffix=".png"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	307 fi
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	308 if [[ $ftype == TIFF ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	309 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	310 suffix=".tiff"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	311 typestring="type=\"image/tiff\""
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	312 fi
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	313
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	314 image=`basename ${myarr[2]}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	315 image=${image%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	316 image="${image}${suffix}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	317 cp ${myarr[2]} ${galaxypath}/${image}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	318
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	319 if [[ ${align} == "none" ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	320 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	321 alignstring=""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	322 alignstring2=""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	323 else
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	324 alignstring="<div float=\"${align}\">"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	325 alignstring2="</div>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	326
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	327 alignstring="align=\"${align}\""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	328 alignstring2=""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	329 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	330
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	331
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	332 if [[ ${zoomlevel} -eq 0 ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	333 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	334 widthstring=""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	335 else
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	336 widthstring="width=\"${zoomlevel}\""
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	337 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	338
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	339 if [[ ${zoomlevel} -eq 0 \|\| ${zoomenable} == "N" ]]
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	340 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	341 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	342 else
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	343 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	344 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	345
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	346 fi
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	347
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	348 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	349 ## Table
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	350 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	351 if [ ${myarr[1]} == "table" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	352 then
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	353
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	354 maxlines=50000
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	355 tsvfile_orig=${myarr[2]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	356 tsvfile="tablehead.tsv"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	357 fname=`basename ${tsvfile_orig}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	358 fname=${fname%.*}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	359 fancy=${myarr[4]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	360 makelinks=${myarr[5]}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	361 #iframeid="iframe$giframecount"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	362 iframeid="iframe-$iframename"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	363
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	364 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	365
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	366 #TODO client side database for large files. For now only display first section of file and add download link
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	367 numlines=`wc -l ${tsvfile_orig} \|cut -d" " -f1`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	368
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	369 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	370
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	371 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	372 awk 'BEGIN{
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	373 FS="\t"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	374 OFS="\t"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	375 }{
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	376 if((index($0,"#")==1 && index($0,"#CHROM")!=1) \|\| $0==""){
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	377 headerlines++
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	378 }
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	379 else print $0
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	380
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	381 }END{}' tsvtmpfile > ${tsvfile}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	382
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	383 if [[ $makelinks == "Y" ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	384 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	385 col=${myarr[6]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	386 prefix=${myarr[7]}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	387 suffix=${myarr[8]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	388 urlitems=${myarr[9]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	389 minw=${myarr[10]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	390 minh=${myarr[11]}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	391 suffix=${suffix/emptycol/}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	392 suffix=${suffix/==quote==/&}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	393 prefix=${prefix/emptycol/}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	394 prefix=${prefix/==quote==/&}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	395 prefix=${prefix/==colon==/:}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	396
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	397 # unpack archive of files to link to if present
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	398 if [[ ${urlitems} != None ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	399 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	400 oldfname=$fname
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	401 decompressArchive ${urlitems}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	402 prefix=archive_${fname}/${prefix}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	403 fname=$oldfname
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	404 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	405
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	406
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	407 #edit the table to include links
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	408 awk 'BEGIN{
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	409 FS="\t"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	410 OFS="\t"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	411 url="'"$prefix"'"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	412 url2="'"$suffix"'"
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	413 iframeid="'"$iframeid"'"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	414 prefix="<a href=\42"
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	415 suffix="\42 onclick=\42resizeIframe("iframeid")\42>"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	416 col="'"$col"'"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	417 end="</a>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	418 }{
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	419 if(FNR==1)
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	420 print $0
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	421 else{
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	422 $col=prefix""url""$col""url2""suffix""$col""end
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	423 print $0
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	424 }
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	425 }END{}' ${tsvfile} > ${tsvfile}2
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	426
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	427 else
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	428 minw=${myarr[6]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	429 minh=${myarr[7]}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	430 cp ${tsvfile} ${tsvfile}2
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	431 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	432
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	433 #iframecount=$[$iframecount+1]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	434
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	435 if [ $fancy == "Y" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	436 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	437 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	438 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>"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	439
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	440 else
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	441 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	442 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>"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	443
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	444 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	445
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	446 if [[ $numlines -gt ${maxlines} ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	447 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	448 tablename=`basename ${tsvfile_orig}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	449 cp ${tsvfile_orig} ${galaxypath}/$tablename
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	450 contentline="${contentline}<br/>\nLarge tables will be supported soon. The first ${maxlines} lines are shown here, and you can download the full file <a href=\"${tablename}\">here</a>."
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	451 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	452 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	453
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	454 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	455 ## PDF
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	456 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	457 if [[ ${myarr[1]} == "pdf" ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	458 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	459 pdffile=${myarr[2]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	460 fname=`basename ${pdffile}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	461 fname=${fname%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	462 pdfname="${fname}.pdf"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	463 cp ${pdffile} "${galaxypath}/${pdfname}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	464
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	465 width=1000
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	466 height=800
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	467 echo -e "<html><body><object data=\"${pdfname}\" type=\"application/pdf\" width=\"$width\" height=\"$height\"><embed src=\"${pdfname}\" type=\"application/pdf\" /><p>It appears you have no PDF plugin for your browser. No biggie... you can <a href=\"${pdfname}\">click here to download the PDF file.</a></p></object></body></html>" > "${galaxypath}/${fname}.html"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	468 width=$[$width+10]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	469 height=$[$height+10]
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	470 contentline="${contentline}\n<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	471
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	472 fi
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	473
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	474 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	475 ## HTML
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	476 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	477 if [[ ${myarr[1]} == "htmlfile" ]]
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	478 then
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	479 htmlfile=${myarr[2]}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	480 height=${myarr[4]}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	481 fname=`basename ${htmlfile}`
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	482 fname=${fname%.dat}
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	483 htmlname="${fname}.html"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	484 cp ${htmlfile} "${galaxypath}/${htmlname}"
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	485
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	486 apiid=${myarr[5]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	487 isireport=${myarr[6]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	488 localhost=${myarr[7]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	489 proxy=${myarr[8]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	490 localhost=${localhost//==colon==/:}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	491 localhost=${localhost//==fslash==/\/}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	492 if [[ ${isireport} == "Y" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	493 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	494 #cp ${localhost}/datasets/${apiid}/* "${galaxypath}/tst"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	495 htmlname="/${proxy}/datasets/${apiid}/display/"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	496 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	497
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	498 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	499 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	500
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	501
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	502 if [[ ${myarr[1]} == "htmlpage" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	503 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	504 url=${myarr[2]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	505 url=${url//==colon==/:}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	506 url=${url//==fslash==//}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	507 height=${myarr[4]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	508 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	509 fi
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	510
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	511 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	512 ## Web Link
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	513 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	514 if [ ${myarr[1]} == "weblink" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	515 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	516 url=${myarr[2]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	517 linktext=${myarr[4]}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	518
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	519 echo -n "$url" > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	520 url=`base64 -d tmpfileb64`
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	521
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	522 echo -n "$linktext" > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	523 linktext=`base64 -d tmpfileb64`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	524
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	525 if [[ -z $linktext ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	526 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	527 linktext=$url
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	528 fi
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	529 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	530 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	531
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	532
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	533 ##
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	534 ## Genome Browser
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	535 ##
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	536 if [ ${myarr[1]} == "genomebrowser" ]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	537 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	538
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	539 # parse inputs
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	540
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	541 apiid=${myarr[4]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	542 servername=${myarr[5]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	543 buildver=${myarr[2]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	544
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	545
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	546 region=${myarr[6]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	547
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	548
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	549 echo -n "$region" > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	550 region=`base64 -d tmpfileb64`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	551
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	552
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	553 initialchrom=${region%:*}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	554 initialrange=${region#*:}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	555
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	556 initialstart=${initialrange%-*}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	557 initialend=${initialrange#*-}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	558
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	559
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	560 #TODO
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	561 ftype="vcf"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	562
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	563 servername=${servername/==colon==/:}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	564
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	565 ## parse and prepare all tracks
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	566 gbcount=$[$gbcount+1]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	567 gbfilelist=${tracklist}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	568 userTracks=""
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	569 #IFS=',' read -a gbfilearray <<< ${gbfilelist}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	570 gbfilearray=(${gbfilelist//,/ })
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	571 for gbfile in "${gbfilearray[@]}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	572 do
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	573 # gbfile is in format "browsernum:file"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	574 #IFS=':' read -a gbfileinfo <<< ${gbfile}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	575 gbfileinfo=(${gbfile//:/ })
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	576 if [[ ${gbfileinfo[0]} == $gbcount ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	577 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	578
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	579 ftype=${gbfileinfo[3]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	580
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	581 gbfilename=${gbfileinfo[1]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	582 gbfilelabel=${gbfileinfo[2]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	583 gbfilelabel=${gbfilelabel//==space==/ }
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	584 gbfilelabel=${gbfilelabel//==bopen==/(}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	585 gbfilelabel=${gbfilelabel//==bclose==/)}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	586 fname=`basename ${gbfilename}`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	587 fname=${fname%.dat}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	588
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	589 if [[ $ftype == "vcftabix" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	590 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	591 newgbfilename="${fname}.vcf"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	592
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	593
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	594 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	595 bgzip "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	596 tabix -f -p vcf "${galaxypath}/${newgbfilename}.gz"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	597
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	598 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	599 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	600 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	601 tier_type: 'tabix',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	602 payload: 'vcf'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	603 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	604 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	605
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	606 if [[ $ftype == "vcfmemstore" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	607 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	608 newgbfilename="${fname}.vcf"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	609
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	610
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	611 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	612 #bgzip "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	613 #tabix -p vcf "${galaxypath}/${newgbfilename}.gz"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	614
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	615 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	616 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	617 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	618 tier_type: 'memstore',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	619 payload: 'vcf'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	620 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	621 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	622
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	623 if [[ $ftype == "bam" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	624 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	625 newgbfilename="${fname}.bam"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	626
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	627 # link to bam instead of copying
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	628 ln -s ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	629 samtools index "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	630
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	631 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	632 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	633 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	634 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	635
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	636 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	637
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	638 if [[ $ftype == "bigbed" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	639 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	640 newgbfilename="${fname}.bigbed"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	641
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	642 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	643 #bgzip "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	644 #tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	645
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	646 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	647 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	648 bwgURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	649 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	650
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	651 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	652
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	653 if [[ $ftype == "bedtabix" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	654 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	655 newgbfilename="${fname}.bed"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	656
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	657 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	658 bgzip "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	659 tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	660
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	661 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	662 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	663 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	664 tier_type: 'tabix',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	665 payload: 'bed'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	666 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	667
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	668 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	669
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	670 if [[ $ftype == "bedmemstore" ]]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	671 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	672 newgbfilename="${fname}.bed"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	673
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	674 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	675 #bgzip "${galaxypath}/${newgbfilename}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	676 #tabix -p bed "${galaxypath}/${newgbfilename}.gz"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	677
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	678 userTracks="${userTracks},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	679 {name: '${gbfilelabel}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	680 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	681 tier_type: 'memstore',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	682 payload: 'bed'}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	683 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	684
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	685 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	686 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	687 done
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	688
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	689
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	690
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	691 if [ ${buildver} == "hg18" ]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	692 then
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	693 coordSystem="coordSystem: {
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	694 speciesName: 'Human',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	695 taxon: 9606,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	696 auth: 'NCBI',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	697 version: '36',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	698 ucscName: 'hg18'
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	699 },"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	700
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	701 chains="chains: {
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	702 hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	703 {
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	704 speciesName: 'Human',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	705 taxon: 9606,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	706 auth: 'GRCh',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	707 version: 37
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	708 })
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	709 },"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	710
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	711 genesTrack="{name: 'Genes',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	712 desc: 'Gene structures from Ensembl 54',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	713 uri: 'https://www.biodalliance.org/das/hsa_54_36p/',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	714 collapseSuperGroups: true,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	715 provides_karyotype: true,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	716 provides_search: true,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	717 provides_entrypoints: true,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	718 maxbins: false}, "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	719
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	720 repeatsTrack="{name: 'Repeats',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	721 desc: 'Repeat annotation from Ensembl 59',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	722 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	723 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	724
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	725
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	726 # default is hg19
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	727 else
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	728 coordSystem="coordSystem: {
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	729 speciesName: 'Human',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	730 taxon: 9606,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	731 auth: 'NCBI',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	732 version: '37',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	733 ucscName: 'hg19'
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	734 },"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	735
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	736 chains=""
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	737
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	738 genesTrack="{name: 'Genes',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	739 desc: 'Gene structures from GENCODE 19',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	740 bwgURI: 'https://www.biodalliance.org/datasets/gencode.bb',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	741 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	742 collapseSuperGroups: true,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	743 trixURI: 'https://www.biodalliance.org/datasets/geneIndex.ix'},"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	744
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	745 repeatsTrack="{name: 'Repeats',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	746 desc: 'Repeat annotation from Ensembl 59',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	747 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	748 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'},"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	749
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	750 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	751
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	752 contentline="${contentline}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	753 <script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script>
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	754 <script language=\"javascript\">
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	755 new Browser({
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	756 chr: '$initialchrom',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	757 viewStart: $initialstart,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	758 viewEnd: $initialend,
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	759 cookieKey: 'human',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	760 pageName: 'svgHolder${gbcount}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	761 ${coordSystem}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	762
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	763 ${chains}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	764 sources: [{name: 'Genome',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	765 twoBitURI: 'https://www.biodalliance.org/datasets/${buildver}.2bit',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	766 tier_type: 'sequence'},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	767 ${genesTrack},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	768 ${repeatsTrack},
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	769 {name: 'Conservation',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	770 desc: 'Conservation',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	771 bwgURI: 'https://www.biodalliance.org/datasets/phastCons46way.bw',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	772 noDownsample: true}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	773 ${userTracks}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	774 ],
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	775
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	776
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	777
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	778
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	779 browserLinks: {
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	780 Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	781 UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}',
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	782 Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}'
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	783 }
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	784
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	785 });
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	786 </script>
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	787
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	788 <div id=\"svgHolder${gbcount}\"></div>
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	789 "
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	790 fi
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	791
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	792 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	793 ## Link to Dataset
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	794 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	795 if [ ${myarr[1]} == "link" ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	796 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	797 linkfile=${myarr[2]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	798 apiid=${myarr[4]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	799 isireport=${myarr[5]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	800 linkfilename=`basename ${linkfile}`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	801 linktext=${myarr[6]}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	802
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	803 localhost=${myarr[7]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	804 proxy=${myarr[8]}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	805 localhost=${localhost//==colon==/:}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	806 localhost=${localhost//==fslash==/\/}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	807
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	808 #check for some basic filetypes
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	809 ftype=`file $linkfile`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	810 if [[ $ftype == HTML ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	811 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	812 linkfilename=${linkfilename%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	813 linkfilename=${linkfilename}.html
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	814 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	815 if [[ $ftype == PNG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	816 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	817 linkfilename=${linkfilename%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	818 linkfilename=${linkfilename}.png
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	819 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	820 if [[ $ftype == SVG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	821 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	822 linkfilename=${linkfilename%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	823 linkfilename=${linkfilename}.svg
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	824 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	825 if [[ $ftype == JPEG ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	826 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	827 linkfilename=${linkfilename%.dat}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	828 linkfilename=${linkfilename}.jpg
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	829 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	830
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	831
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	832 if [[ ${isireport} == "Y" ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	833 then
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	834 linkfilename="/${proxy}/datasets/${apiid}/display/"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	835 else
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	836 cp ${linkfile} "${galaxypath}/${linkfilename}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	837 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	838
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	839 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	840 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	841
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	842 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	843 ## Links to Archive Contents
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	844 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	845 if [[ ${myarr[1]} == "links" ]]
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	846 then
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	847 archive=${myarr[2]}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	848 decompressArchive $archive
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	849
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	850 # add links to webpage
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	851 # separate line for each folder, files within folder on same line
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	852 for linkfile in `ls ${galaxypath}/archive_${fname}/ \|sort -V`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	853 do
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	854 #echo "<br/> ->making link to file: $linkfile "
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	855 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	856 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	857 #echo "<br/> ->is directory, entering: $linkfile "
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	858 #ls ${galaxypath}/archive_${fname}/$linkfile
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	859 contentline="${contentline}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	860 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile \| sort -V`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	861 do
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	862 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	863 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	864 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	865 #echo "<br/> ->is file, making link: $linkfile "
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	866 label=`basename $linkfile2`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	867 label=${label%.*}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	868 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n "
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	869 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	870 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	871 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	872 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	873 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	874 label=${label%.*}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	875 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	876 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	877 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	878
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	879
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	880 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	881
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	882 if [[ ${myarr[3]} == "Y" ]]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	883 then
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	884 contentline="${contentline}<br/>\n"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	885 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	886 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	887 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	888
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	889 echo "${contentline}"
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	890
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	891
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	892 }
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	893
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	894 ##
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	895 ## Create HTML content for iReport
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	896 ##
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	897 createMainPage (){
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	898 #export IFRAMECNT=1
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	899 page=$1
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	900 tabtitles=$2 # comma-separated list of tab titles
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	901 tabitems=$3 # colon-sparated list of tabs specifications
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	902 #giframecount=1 # keep track of number of iFrames so that they can be referenced by ID
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	903 minwidth=$4 # width of page
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	904 gbtracks=$5 # genome browser track information
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	905
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	906 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	907 # create correct number of tabs
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	908 count=0
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	909
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	910 tabtitles=${tabtitles/,/}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	911 tabtitles=${tabtitles//,/ }
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	912 echo $tabtitles
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	913
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	914 tabcount=0
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	915 for tabt in $tabtitles
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	916 do
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	917 echo -n $tabt > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	918 thistabtitle=`base64 -d tmpfileb64`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	919 newtabtitles+=" $thistabtitle"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	920 tabcount=$[tabcount+1]
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	921 done
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	922
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	923 echo $newtabtitles
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	924
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	925 tabslist="<ul>\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	926 mytabs=""
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	927
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	928 for title in $newtabtitles
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	929 do
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	930 # Create list of tabs
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	931 count=$[count+1]
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	932 title2=${title//==space==/ }
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	933 title2=${title2//==dollar==/$}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	934 title2=${title2//==colon==/}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	935 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	936
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	937 # Create tabs with content
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	938 tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks")
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	939 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	940 mytabs="${mytabs}${tabcontent}"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	941 mytabs="${mytabs}\n</div>\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	942 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	943 tabslist="${tabslist}</ul>"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	944
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	945 ## Output the webpage
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	946 echo -e "<!doctype html>
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	947 <head>
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	948 <meta charset=\"utf-8\">
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	949 <title>iReport</title>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	950 <link rel=\"stylesheet\" href=\"jquery-ui.css\">
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	951 <link rel=\"stylesheet\" href=\"ireport_css.css\">
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	952 <link rel=\"stylesheet\" href=\"md.css\">
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	953 <script type=\"text/javascript\" src=\"jquery-1.10.2.js\"></script>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	954 <script type=\"text/javascript\" src=\"jquery-ui.js\"></script>
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	955 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script>
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	956 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script>
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	957 <script type=\"text/javascript\" src=\"ireport_jquery.js\"></script>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	958 <script type=\"text/javascript\" src=\"ireport_javascript.js\"></script>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	959 </head>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	960 <body>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	961 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\">
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	962 $tabslist
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	963
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	964 $mytabs
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	965 </div>
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 1 diff changeset	966 </body>
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	967 </html>" > $page
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	968 }

Mercurial > repos > saskia-hiltemann > ireport

annotate createHTML.sh @ 8:86219e4aa239 draft