annotate createHTML.sh @ 2:3c160414da2e default tip

initial upload
author shiltemann
date Thu, 26 Feb 2015 14:05:23 +0100
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1 gbcount=0
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2
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3 ##
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4 ## Create Cover Page
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5 ##
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6 function makeIntroPage ( ){
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7 echo "Creating Intro Page"
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8 title="$1"
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9 coverimage=$2
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10 link=$3
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11 htmlout=$4
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12 zipireport=$5
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13
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14 echo -e "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">
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15 <html>
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16 <head>
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17 </head>
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18 <body>
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19 <br/>
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20 <br/>
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21 <center>
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22 <b><font size=\"15\"> iReport: ${title} </font></b><br/>
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23 <br/>
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24 <br/>
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25 <a href=\"$link\"> Click here to view report </a> <br/><br/>
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26 <a href=\"$link\"> <img src="$coverimage" width=\"50%\" alt=\"loading image..\"/> </a><br/><br/>
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27 <a href=\"$zipireport\"> Click here to download a copy of this iReport </a> <br/><br/>
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28 </center>
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29 </body>
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30 </html>" > $htmlout
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31
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32 }
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33
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34 ##
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35 ## Decompress archive fiels
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36 ## -> will detect archive formats: zip, tar, gzip, tar.gz, bzip2
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37 ## -> input: path to archive
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38 ## -> files will be located in ${galaxypath}/archive_${fname}/
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39 ##
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40 function decompressArchive (){
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41 archive=$1
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42
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43 fname=`basename ${archive}`
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44 fname=${fname%.dat}
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45 ftype=`file $archive`
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46
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47 if [[ ! -d ${galaxypath}/archive_${fname}/ ]]
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48 then
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49 mkdir ${galaxypath}/archive_${fname}/
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50
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51 #echo "archive type: `file $archive`"
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52 # decompress archive
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53 if [[ $ftype == *Zip* ]]
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54 then
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55 #echo "detected zip file"
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56 cp $archive ${galaxypath}/archive_${fname}/${fname}.zip
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57 wd=`pwd`
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58 cd ${galaxypath}/archive_${fname}/
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59 unzip -q ${fname}.zip
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60 rm ${fname}.zip
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61 cd $wd
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62 fi
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63 if [[ $ftype == *tar* ]]
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64 then
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65 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar
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66 wd=`pwd`
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67 cd ${galaxypath}/archive_${fname}/
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68 tar xf ${fname}.tar
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69 rm ${fname}.tar
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70 cd $wd
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71 fi
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72 if [[ $ftype == *gzip* ]]
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73 then
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74 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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75 gunzip ${galaxypath}/archive_${fname}/${fname}.gz
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76 #ls ${galaxypath}/archive_${fname}/
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77
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78 # check for tar.gz
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79 ftype=`file ${galaxypath}/archive_${fname}/${fname}`
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80 if [[ $ftype == *tar* ]]
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81 then
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82 # turns out it was tar.gz
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83 rm -Rf ${galaxypath}/archive_${fname}/*
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84 ls ${galaxypath}/archive_${fname}/
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85 cp $archive ${galaxypath}/archive_${fname}/${fname}.tar.gz
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86
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87 wd=`pwd`
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88 cd ${galaxypath}/archive_${fname}/
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89 tar xzf ${fname}.tar.gz
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90 cd $wd
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91 fi
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92 wait
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93 rm -f ${galaxypath}/archive_${fname}/*.tar
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94 rm -f ${galaxypath}/archive_${fname}/*.tar.gz
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95 fi
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96 if [[ $ftype == *bzip2* ]]
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97 then
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98 cp $archive ${galaxypath}/archive_${fname}/${fname}.gz
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99 gunzip2 ${galaxypath}/archive_${fname}/${fname}.gz
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100 fi
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101 fi
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102 }
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103
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104 ##
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105 ## Create HTML content for the tabs specified by user
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106 ##
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107 function makeTabContent ( ){
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108 tab=$1 # name of current tab
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109 itemslist=$2 # list of all items
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110 tracklist=$3 # genome browser tracks info
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111 contentline="" # HTML code for tab
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112 imgcount=0 # keep track of the number of images on the current tab
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113 iframecount=0
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114
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115 for item in $itemslist
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116 do
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117 ## Parse items lists
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118 item=${item/::/:emptycol:}
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119 declare -a myarr=(`echo $item |sed 's/:/ /g'`)
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120
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121 ## Create the tab contents HTML code
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122 if [ ${myarr[0]} == $tab ]
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123 then
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124
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125 ##
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126 ## Text Field
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127 ##
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128 if [ ${myarr[1]} == "text" ]
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129 then
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130 text=${myarr[2]}
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131 md=${myarr[4]}
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132
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133 # if markdown, convert to html
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134 if [ $md == "Y" ]
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135 then
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136 ## resubstitute sanitized charachters
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137 text=${text//==space==/ }
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138 text=${text//==colon==/:}
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139 text=${text//==comma==/,}
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140 text=${text//==slash==/\/}
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141 text=${text//==lt==/<}
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142 text=${text//==gt==/>}
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143 text=${text//==apos==/\'}
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144 text=${text//==quote==/\"}
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145 text=${text//==backtick==/\`}
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146 text=${text//==dollar==/$}
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147 text=${text//==bar==/|}
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148 text=${text//&&/&}
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149 text=${text//\\n/\\n}
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150 text=${text//\\t/\\t}
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151 text=${text//\&r\&n/\\n}
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152 text=${text//\&r/\\n}
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153 text=${text//\&n/\\n}
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154 text=${text//\&c/:}
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155
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156
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157 ## convert markdown in textfield to html
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158 echo -e "$text" > mytext.md
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159
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160 if [ -z `type -p pandoc` ]
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161 then
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162 # pandoc missing
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163 ${repositorypath}/Markdown/markdown2.py mytext.md > mytext.html
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164
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165 else
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166 # pandoc exists
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167 pandoc -f markdown -o mytext.html mytext.md
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168 pandoc -f markdown -o standalone.html -s mytext.md
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169
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170 #get css generated by pandoc and add as scoped attribute (HTML5)
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171 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
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172 fi
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173
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174 markdowntext=$(cat mytext.html)
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175 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n"
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176
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177 else # If not markdown, print verbatim (with exception of few html tags)
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178
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179 ## allow some html formatting tags
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180 text=${text//==lt==strong==gt==/<strong>} # search for strong tags
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181 text=${text//==lt====slash==strong==gt==/<\/strong>} # search for strong tags
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182 text=${text//==lt==em==gt==/<em>} # search for strong tags
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183 text=${text//==lt====slash==em==gt==/<\/em>} # search for strong tags
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184
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185 text=${text//==lt==b==gt==/<strong>} # search for strong tags
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186 text=${text//==lt====slash==b==gt==/<\/strong>} # search for strong tags
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187 text=${text//==lt==i==gt==/<em>} # search for strong tags
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188 text=${text//==lt====slash==i==gt==/<\/em>} # search for strong tags
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189
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190 text=${text//==lt==br==gt==/<br\/>} # search for strong tags
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191 text=${text//==lt====br==slash==gt==/<br\/>} # search for strong tags
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192 text=${text//==lt==h1==gt==/<h1>} # search for h1-h6 tags
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193 text=${text//==lt==h2==gt==/<h2>} # search for h1-h6 tags
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194 text=${text//==lt==h3==gt==/<h3>} # search for h1-h6 tags
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195 text=${text//==lt==h4==gt==/<h4>} # search for h1-h6 tags
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196 text=${text//==lt==h5==gt==/<h5>} # search for h1-h6 tags
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197 text=${text//==lt==h6==gt==/<h6>} # search for h1-h6 tags
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198 text=${text//==lt====slash==h1==gt==/<\/h1>} # search for h1-h6 closing tags
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199 text=${text//==lt====slash==h2==gt==/<\/h2>} # search for h1-h6 closing tags
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200 text=${text//==lt====slash==h3==gt==/<\/h3>} # search for h1-h6 closing tags
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201 text=${text//==lt====slash==h4==gt==/<\/h4>} # search for h1-h6 closing tags
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202 text=${text//==lt====slash==h5==gt==/<\/h5>} # search for h1-h6 closing tags
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203 text=${text//==lt====slaxh==h6==gt==/<\/h6>} # search for h1-h6 closing tags
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204
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205 ## display everything else verbatim
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206 text=${text//==space==/ }
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207 text=${text//==colon==/:}
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208 text=${text//==comma==/,}
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209 text=${text//==slash==/\/}
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210 text=${text//==lt==/&lt;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
211 text=${text//==gt==/&gt;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
212 text=${text//==apos==/&apos;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
213 text=${text//==quote==/&quot;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
214 text=${text//&&/&amp;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
215 text=${text//\\n/<br/>}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
216 text=${text//\\t/&emsp;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
217 text=${text//\&r\&n/<br/>}
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shiltemann
parents:
diff changeset
218 text=${text//\&r/<br/>}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
219 text=${text//\&n/<br/>}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
220 text=${text//\&c/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
221 text=${text//==backtick==/&#96;}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
222 text=${text//==dollar==/$}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
223 text=${text//==bar==/|}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
224 contentline="${contentline}\n${text}\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
225 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
226
3c160414da2e initial upload
shiltemann
parents:
diff changeset
227
3c160414da2e initial upload
shiltemann
parents:
diff changeset
228 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
229
3c160414da2e initial upload
shiltemann
parents:
diff changeset
230 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
231 ## Text File
3c160414da2e initial upload
shiltemann
parents:
diff changeset
232 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
233 if [ ${myarr[1]} == "textfile" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
234 then
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shiltemann
parents:
diff changeset
235 tfile=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
236 md=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
237 fname=`basename ${tfile}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
238 fname=${fname%.*}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
239 fname="${fname}.txt"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
240 cp ${tfile} "${galaxypath}/${fname}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
241
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shiltemann
parents:
diff changeset
242 #estimate height for iframe based on number oflines in the file
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shiltemann
parents:
diff changeset
243 numlines=`wc -l ${tfile} | cut -d" " -f1`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
244 minheight=$[$numlines*17]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
245
3c160414da2e initial upload
shiltemann
parents:
diff changeset
246 # if markdown, convert to html
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shiltemann
parents:
diff changeset
247 if [ $md == "Y" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
248 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
249
3c160414da2e initial upload
shiltemann
parents:
diff changeset
250 if [ -z `type -p pandoc` ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
251 then
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shiltemann
parents:
diff changeset
252 # pandoc missing
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shiltemann
parents:
diff changeset
253 ${repositorypath}/Markdown/markdown2.py ${tfile} > mytext.html
3c160414da2e initial upload
shiltemann
parents:
diff changeset
254
3c160414da2e initial upload
shiltemann
parents:
diff changeset
255 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
256 # pandoc exists
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shiltemann
parents:
diff changeset
257 pandoc -o mytext.html ${tfile}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
258 pandoc -o standalone.html -s ${tfile}
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shiltemann
parents:
diff changeset
259
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shiltemann
parents:
diff changeset
260 # get css generated by pandoc and add as scoped attribute (HTML5)
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shiltemann
parents:
diff changeset
261 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
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shiltemann
parents:
diff changeset
262
3c160414da2e initial upload
shiltemann
parents:
diff changeset
263 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
264
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shiltemann
parents:
diff changeset
265 markdowntext=$(cat mytext.html)
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shiltemann
parents:
diff changeset
266 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
267 else
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shiltemann
parents:
diff changeset
268 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
269 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
270 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
271
3c160414da2e initial upload
shiltemann
parents:
diff changeset
272 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
273 ## Image
3c160414da2e initial upload
shiltemann
parents:
diff changeset
274 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
275 if [ ${myarr[1]} == "image" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
276
3c160414da2e initial upload
shiltemann
parents:
diff changeset
277 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
278 imgcount=$[$imgcount+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
279 #restore file suffix for html
3c160414da2e initial upload
shiltemann
parents:
diff changeset
280 ftype=`file ${myarr[2]}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
281 zoomlevel=${myarr[4]}
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shiltemann
parents:
diff changeset
282 zoomenable=${myarr[5]}
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shiltemann
parents:
diff changeset
283 align=${myarr[6]}
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shiltemann
parents:
diff changeset
284 #####echo "zoomenable:${zoomenable}, align:${align}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
285 if [[ $ftype == *JPEG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
286 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
287 suffix=".jpg"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
288 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
289 if [[ $ftype == *SVG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
290 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
291 suffix=".svg"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
292 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
293 if [[ $ftype == *PNG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
294 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
295 suffix=".png"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
296 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
297
3c160414da2e initial upload
shiltemann
parents:
diff changeset
298 image=`basename ${myarr[2]}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
299 image=${image%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
300 image="${image}${suffix}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
301 cp ${myarr[2]} ${galaxypath}/${image}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
302
3c160414da2e initial upload
shiltemann
parents:
diff changeset
303 if [[ ${align} == "none" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
304 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
305 alignstring=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
306 alignstring2=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
307 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
308 alignstring="<div float=\"${align}\">"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
309 alignstring2="</div>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
310
3c160414da2e initial upload
shiltemann
parents:
diff changeset
311 alignstring="align=\"${align}\""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
312 alignstring2=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
313 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
314
3c160414da2e initial upload
shiltemann
parents:
diff changeset
315
3c160414da2e initial upload
shiltemann
parents:
diff changeset
316 if [[ ${zoomlevel} -eq 0 ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
317 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
318 widthstring=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
319 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
320 widthstring="width=\"${zoomlevel}\""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
321 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
322
3c160414da2e initial upload
shiltemann
parents:
diff changeset
323 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
324 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
325 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
326 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
327 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
328 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
329
3c160414da2e initial upload
shiltemann
parents:
diff changeset
330 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
331
3c160414da2e initial upload
shiltemann
parents:
diff changeset
332 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
333 ## Table
3c160414da2e initial upload
shiltemann
parents:
diff changeset
334 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
335 if [ ${myarr[1]} == "table" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
336 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
337
3c160414da2e initial upload
shiltemann
parents:
diff changeset
338 maxlines=50000
3c160414da2e initial upload
shiltemann
parents:
diff changeset
339 tsvfile_orig=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
340 tsvfile="tablehead.tsv"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
341 fname=`basename ${tsvfile_orig}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
342 fname=${fname%.*}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
343 fancy=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
344 makelinks=${myarr[5]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
345 iframeid="iframe"$iframecount
3c160414da2e initial upload
shiltemann
parents:
diff changeset
346 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
347
3c160414da2e initial upload
shiltemann
parents:
diff changeset
348 #TODO client side database for large files. For now only display first section of file and add download link
3c160414da2e initial upload
shiltemann
parents:
diff changeset
349 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
350
3c160414da2e initial upload
shiltemann
parents:
diff changeset
351 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
3c160414da2e initial upload
shiltemann
parents:
diff changeset
352
3c160414da2e initial upload
shiltemann
parents:
diff changeset
353 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
3c160414da2e initial upload
shiltemann
parents:
diff changeset
354 awk 'BEGIN{
3c160414da2e initial upload
shiltemann
parents:
diff changeset
355 FS="\t"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
356 OFS="\t"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
357 }{
3c160414da2e initial upload
shiltemann
parents:
diff changeset
358 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){
3c160414da2e initial upload
shiltemann
parents:
diff changeset
359 headerlines++
3c160414da2e initial upload
shiltemann
parents:
diff changeset
360 }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
361 else print $0
3c160414da2e initial upload
shiltemann
parents:
diff changeset
362
3c160414da2e initial upload
shiltemann
parents:
diff changeset
363 }END{}' tsvtmpfile > ${tsvfile}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
364
3c160414da2e initial upload
shiltemann
parents:
diff changeset
365 if [[ $makelinks == "Y" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
366 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
367 col=${myarr[6]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
368 prefix=${myarr[7]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
369 suffix=${myarr[8]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
370 urlitems=${myarr[9]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
371 minw=${myarr[10]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
372 suffix=${suffix/emptycol/}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
373 suffix=${suffix/==quote==/&}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
374 prefix=${prefix/emptycol/}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
375 prefix=${prefix/==quote==/&}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
376 prefix=${prefix/==colon==/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
377
3c160414da2e initial upload
shiltemann
parents:
diff changeset
378 # unpack archive of files to link to if present
3c160414da2e initial upload
shiltemann
parents:
diff changeset
379 if [[ ${urlitems} != None ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
380 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
381 oldfname=$fname
3c160414da2e initial upload
shiltemann
parents:
diff changeset
382 decompressArchive ${urlitems}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
383 prefix=archive_${fname}/${prefix}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
384 fname=$oldfname
3c160414da2e initial upload
shiltemann
parents:
diff changeset
385 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
386
3c160414da2e initial upload
shiltemann
parents:
diff changeset
387
3c160414da2e initial upload
shiltemann
parents:
diff changeset
388 #edit the table to include links
3c160414da2e initial upload
shiltemann
parents:
diff changeset
389 awk 'BEGIN{
3c160414da2e initial upload
shiltemann
parents:
diff changeset
390 FS="\t"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
391 OFS="\t"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
392 url="'"$prefix"'"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
393 url2="'"$suffix"'"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
394 iframeid="'"$iframeid"'"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
395 prefix="<a href=\42"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
396 suffix="\42 onclick=\42resizeIframe("iframeid")\42>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
397 col="'"$col"'"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
398 end="</a>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
399 }{
3c160414da2e initial upload
shiltemann
parents:
diff changeset
400 if(FNR==1)
3c160414da2e initial upload
shiltemann
parents:
diff changeset
401 print $0
3c160414da2e initial upload
shiltemann
parents:
diff changeset
402 else{
3c160414da2e initial upload
shiltemann
parents:
diff changeset
403 $col=prefix""url""$col""url2""suffix""$col""end
3c160414da2e initial upload
shiltemann
parents:
diff changeset
404 print $0
3c160414da2e initial upload
shiltemann
parents:
diff changeset
405 }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
406 }END{}' ${tsvfile} > ${tsvfile}2
3c160414da2e initial upload
shiltemann
parents:
diff changeset
407
3c160414da2e initial upload
shiltemann
parents:
diff changeset
408 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
409 minw=${myarr[6]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
410 cp ${tsvfile} ${tsvfile}2
3c160414da2e initial upload
shiltemann
parents:
diff changeset
411 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
412
3c160414da2e initial upload
shiltemann
parents:
diff changeset
413 iframecount=$[$iframecount+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
414 if [ $fancy == "Y" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
415 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
416 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
3c160414da2e initial upload
shiltemann
parents:
diff changeset
417 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 760px; min-height: 525px; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
418 iframecount=$[$iframecount+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
419 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
420 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
3c160414da2e initial upload
shiltemann
parents:
diff changeset
421 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
422 iframecount=$[$iframecount+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
423 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
424
3c160414da2e initial upload
shiltemann
parents:
diff changeset
425 if [[ $numlines -gt ${maxlines} ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
426 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
427 tablename=`basename ${tsvfile_orig}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
428 cp ${tsvfile_orig} ${galaxypath}/$tablename
3c160414da2e initial upload
shiltemann
parents:
diff changeset
429 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>."
3c160414da2e initial upload
shiltemann
parents:
diff changeset
430 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
431 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
432
3c160414da2e initial upload
shiltemann
parents:
diff changeset
433 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
434 ## PDF
3c160414da2e initial upload
shiltemann
parents:
diff changeset
435 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
436 if [[ ${myarr[1]} == "pdf" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
437 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
438 pdffile=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
439 fname=`basename ${pdffile}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
440 fname=${fname%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
441 pdfname="${fname}.pdf"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
442 cp ${pdffile} "${galaxypath}/${pdfname}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
443
3c160414da2e initial upload
shiltemann
parents:
diff changeset
444 width=1000
3c160414da2e initial upload
shiltemann
parents:
diff changeset
445 height=800
3c160414da2e initial upload
shiltemann
parents:
diff changeset
446 echo -e "<html><body><object data=\"${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"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
447 width=$[$width+10]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
448 height=$[$height+10]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
449 contentline="${contentline}\n<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
450
3c160414da2e initial upload
shiltemann
parents:
diff changeset
451 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
452
3c160414da2e initial upload
shiltemann
parents:
diff changeset
453 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
454 ## HTML
3c160414da2e initial upload
shiltemann
parents:
diff changeset
455 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
456 if [[ ${myarr[1]} == "htmlfile" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
457 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
458 htmlfile=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
459 height=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
460 fname=`basename ${htmlfile}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
461 fname=${fname%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
462 htmlname="${fname}.html"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
463 cp ${htmlfile} "${galaxypath}/${htmlname}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
464
3c160414da2e initial upload
shiltemann
parents:
diff changeset
465 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
466 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
467
3c160414da2e initial upload
shiltemann
parents:
diff changeset
468
3c160414da2e initial upload
shiltemann
parents:
diff changeset
469 if [[ ${myarr[1]} == "htmlpage" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
470 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
471 url=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
472 url=${url//==colon==/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
473 url=${url//==fslash==//}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
474 height=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
475
3c160414da2e initial upload
shiltemann
parents:
diff changeset
476 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
477 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
478
3c160414da2e initial upload
shiltemann
parents:
diff changeset
479 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
480 ## Web Link
3c160414da2e initial upload
shiltemann
parents:
diff changeset
481 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
482 if [ ${myarr[1]} == "weblink" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
483 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
484 url=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
485 linktext=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
486 url=${url/==colon==/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
487 url=${url/==quote==/&}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
488
3c160414da2e initial upload
shiltemann
parents:
diff changeset
489 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
490 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
491
3c160414da2e initial upload
shiltemann
parents:
diff changeset
492
3c160414da2e initial upload
shiltemann
parents:
diff changeset
493 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
494 ## Genome Browser
3c160414da2e initial upload
shiltemann
parents:
diff changeset
495 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
496 if [ ${myarr[1]} == "genomebrowser" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
497 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
498 # parse inputs
3c160414da2e initial upload
shiltemann
parents:
diff changeset
499
3c160414da2e initial upload
shiltemann
parents:
diff changeset
500 apiid=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
501 servername=${myarr[5]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
502 buildver=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
503
3c160414da2e initial upload
shiltemann
parents:
diff changeset
504 #TODO
3c160414da2e initial upload
shiltemann
parents:
diff changeset
505 ftype="vcf"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
506
3c160414da2e initial upload
shiltemann
parents:
diff changeset
507 servername=${servername/==colon==/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
508
3c160414da2e initial upload
shiltemann
parents:
diff changeset
509 ## parse and prepare all tracks
3c160414da2e initial upload
shiltemann
parents:
diff changeset
510 gbcount=$[$gbcount+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
511 gbfilelist=${tracklist}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
512 userTracks=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
513 #IFS=',' read -a gbfilearray <<< ${gbfilelist}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
514 gbfilearray=(${gbfilelist//,/ })
3c160414da2e initial upload
shiltemann
parents:
diff changeset
515 for gbfile in "${gbfilearray[@]}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
516 do
3c160414da2e initial upload
shiltemann
parents:
diff changeset
517 # gbfile is in format "browsernum:file"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
518 #IFS=':' read -a gbfileinfo <<< ${gbfile}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
519 gbfileinfo=(${gbfile//:/ })
3c160414da2e initial upload
shiltemann
parents:
diff changeset
520 if [[ ${gbfileinfo[0]} == $gbcount ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
521 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
522
3c160414da2e initial upload
shiltemann
parents:
diff changeset
523 ftype=${gbfileinfo[3]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
524 if [ $ftype == "vcf" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
525 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
526 gbfilename=${gbfileinfo[1]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
527 gbfilelabel=${gbfileinfo[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
528 gbfilelabel=${gbfilelabel//==space==/ }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
529 fname=`basename ${gbfilename}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
530 fname=${fname%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
531 newgbfilename="${fname}.vcf"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
532
3c160414da2e initial upload
shiltemann
parents:
diff changeset
533
3c160414da2e initial upload
shiltemann
parents:
diff changeset
534 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
535 bgzip "${galaxypath}/${newgbfilename}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
536 tabix -p vcf "${galaxypath}/${newgbfilename}.gz"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
537
3c160414da2e initial upload
shiltemann
parents:
diff changeset
538 userTracks="${userTracks},
3c160414da2e initial upload
shiltemann
parents:
diff changeset
539 {name: '${gbfilelabel}',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
540 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
541 tier_type: 'tabix',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
542 payload: 'vcf'}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
543 "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
544 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
545
3c160414da2e initial upload
shiltemann
parents:
diff changeset
546 if [ $ftype == "bam" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
547 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
548 gbfilename=${gbfileinfo[1]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
549 gbfilelabel=${gbfileinfo[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
550 gbfilelabel=${gbfilelabel//==space==/ }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
551 fname=`basename ${gbfilename}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
552 fname=${fname%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
553 newgbfilename="${fname}.bam"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
554
3c160414da2e initial upload
shiltemann
parents:
diff changeset
555 # link to bam instead of copying
3c160414da2e initial upload
shiltemann
parents:
diff changeset
556 ln -s ${gbfilename} "${galaxypath}/${newgbfilename}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
557 samtools index "${galaxypath}/${newgbfilename}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
558
3c160414da2e initial upload
shiltemann
parents:
diff changeset
559 userTracks="${userTracks},
3c160414da2e initial upload
shiltemann
parents:
diff changeset
560 {name: '${gbfilelabel}',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
561 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
562 "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
563
3c160414da2e initial upload
shiltemann
parents:
diff changeset
564 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
565 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
566 done
3c160414da2e initial upload
shiltemann
parents:
diff changeset
567
3c160414da2e initial upload
shiltemann
parents:
diff changeset
568
3c160414da2e initial upload
shiltemann
parents:
diff changeset
569
3c160414da2e initial upload
shiltemann
parents:
diff changeset
570 if [ ${buildver} == "hg18" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
571 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
572 coordSystem="coordSystem: {
3c160414da2e initial upload
shiltemann
parents:
diff changeset
573 speciesName: 'Human',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
574 taxon: 9606,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
575 auth: 'NCBI',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
576 version: '36',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
577 ucscName: 'hg18'
3c160414da2e initial upload
shiltemann
parents:
diff changeset
578 },"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
579
3c160414da2e initial upload
shiltemann
parents:
diff changeset
580 chains="chains: {
3c160414da2e initial upload
shiltemann
parents:
diff changeset
581 hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
582 {
3c160414da2e initial upload
shiltemann
parents:
diff changeset
583 speciesName: 'Human',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
584 taxon: 9606,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
585 auth: 'GRCh',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
586 version: 37
3c160414da2e initial upload
shiltemann
parents:
diff changeset
587 })
3c160414da2e initial upload
shiltemann
parents:
diff changeset
588 },"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
589
3c160414da2e initial upload
shiltemann
parents:
diff changeset
590 genesTrack="{name: 'Genes',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
591 desc: 'Gene structures from Ensembl 54',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
592 uri: 'https://www.biodalliance.org/das/hsa_54_36p/',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
593 collapseSuperGroups: true,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
594 provides_karyotype: true,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
595 provides_search: true,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
596 provides_entrypoints: true,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
597 maxbins: false}, "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
598
3c160414da2e initial upload
shiltemann
parents:
diff changeset
599 repeatsTrack="{name: 'Repeats',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
600 desc: 'Repeat annotation from Ensembl 59',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
601 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
602 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
603
3c160414da2e initial upload
shiltemann
parents:
diff changeset
604
3c160414da2e initial upload
shiltemann
parents:
diff changeset
605 # default is hg19
3c160414da2e initial upload
shiltemann
parents:
diff changeset
606 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
607 coordSystem="coordSystem: {
3c160414da2e initial upload
shiltemann
parents:
diff changeset
608 speciesName: 'Human',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
609 taxon: 9606,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
610 auth: 'NCBI',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
611 version: '37',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
612 ucscName: 'hg19'
3c160414da2e initial upload
shiltemann
parents:
diff changeset
613 },"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
614
3c160414da2e initial upload
shiltemann
parents:
diff changeset
615 chains=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
616
3c160414da2e initial upload
shiltemann
parents:
diff changeset
617 genesTrack="{name: 'Genes',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
618 desc: 'Gene structures from GENCODE 19',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
619 bwgURI: 'https://www.biodalliance.org/datasets/gencode.bb',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
620 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
621 collapseSuperGroups: true,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
622 trixURI: 'https://www.biodalliance.org/datasets/geneIndex.ix'},"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
623
3c160414da2e initial upload
shiltemann
parents:
diff changeset
624 repeatsTrack="{name: 'Repeats',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
625 desc: 'Repeat annotation from Ensembl 59',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
626 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
627 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'},"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
628
3c160414da2e initial upload
shiltemann
parents:
diff changeset
629 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
630
3c160414da2e initial upload
shiltemann
parents:
diff changeset
631 contentline="${contentline}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
632 <script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
633 <script language=\"javascript\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
634 new Browser({
3c160414da2e initial upload
shiltemann
parents:
diff changeset
635 chr: '1',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
636 viewStart: 0,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
637 viewEnd: 100000,
3c160414da2e initial upload
shiltemann
parents:
diff changeset
638 cookieKey: 'human',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
639
3c160414da2e initial upload
shiltemann
parents:
diff changeset
640 ${coordSystem}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
641
3c160414da2e initial upload
shiltemann
parents:
diff changeset
642 ${chains}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
643 sources: [{name: 'Genome',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
644 twoBitURI: 'https://www.biodalliance.org/datasets/${buildver}.2bit',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
645 tier_type: 'sequence'},
3c160414da2e initial upload
shiltemann
parents:
diff changeset
646 ${genesTrack},
3c160414da2e initial upload
shiltemann
parents:
diff changeset
647 ${repeatsTrack},
3c160414da2e initial upload
shiltemann
parents:
diff changeset
648 {name: 'Conservation',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
649 desc: 'Conservation',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
650 bwgURI: 'https://www.biodalliance.org/datasets/phastCons46way.bw',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
651 noDownsample: true}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
652 ${userTracks}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
653 ],
3c160414da2e initial upload
shiltemann
parents:
diff changeset
654
3c160414da2e initial upload
shiltemann
parents:
diff changeset
655
3c160414da2e initial upload
shiltemann
parents:
diff changeset
656
3c160414da2e initial upload
shiltemann
parents:
diff changeset
657
3c160414da2e initial upload
shiltemann
parents:
diff changeset
658 browserLinks: {
3c160414da2e initial upload
shiltemann
parents:
diff changeset
659 Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
660 UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}',
3c160414da2e initial upload
shiltemann
parents:
diff changeset
661 Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}'
3c160414da2e initial upload
shiltemann
parents:
diff changeset
662 }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
663
3c160414da2e initial upload
shiltemann
parents:
diff changeset
664 });
3c160414da2e initial upload
shiltemann
parents:
diff changeset
665 </script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
666
3c160414da2e initial upload
shiltemann
parents:
diff changeset
667 <div id=\"svgHolder\"></div>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
668 "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
669 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
670
3c160414da2e initial upload
shiltemann
parents:
diff changeset
671 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
672 ## Link to Dataset
3c160414da2e initial upload
shiltemann
parents:
diff changeset
673 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
674 if [ ${myarr[1]} == "link" ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
675 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
676 linkfile=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
677 apiid=${myarr[4]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
678 isireport=${myarr[5]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
679 linkfilename=`basename ${linkfile}`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
680 linktext=${myarr[6]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
681
3c160414da2e initial upload
shiltemann
parents:
diff changeset
682
3c160414da2e initial upload
shiltemann
parents:
diff changeset
683 #check for some basic filetypes
3c160414da2e initial upload
shiltemann
parents:
diff changeset
684 ftype=`file $linkfile`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
685 if [[ $ftype == *HTML* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
686 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
687 linkfilename=${linkfilename%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
688 linkfilename=${linkfilename}.html
3c160414da2e initial upload
shiltemann
parents:
diff changeset
689 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
690 if [[ $ftype == *PNG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
691 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
692 linkfilename=${linkfilename%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
693 linkfilename=${linkfilename}.png
3c160414da2e initial upload
shiltemann
parents:
diff changeset
694 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
695 if [[ $ftype == *SVG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
696 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
697 linkfilename=${linkfilename%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
698 linkfilename=${linkfilename}.svg
3c160414da2e initial upload
shiltemann
parents:
diff changeset
699 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
700 if [[ $ftype == *JPEG* ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
701 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
702 linkfilename=${linkfilename%.dat}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
703 linkfilename=${linkfilename}.jpg
3c160414da2e initial upload
shiltemann
parents:
diff changeset
704 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
705
3c160414da2e initial upload
shiltemann
parents:
diff changeset
706
3c160414da2e initial upload
shiltemann
parents:
diff changeset
707 if [[ ${isireport} == "Y" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
708 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
709 linkfilename="/datasets/${apiid}/display/"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
710 else
3c160414da2e initial upload
shiltemann
parents:
diff changeset
711 cp ${linkfile} "${galaxypath}/${linkfilename}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
712 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
713
3c160414da2e initial upload
shiltemann
parents:
diff changeset
714 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
715 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
716
3c160414da2e initial upload
shiltemann
parents:
diff changeset
717 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
718 ## Links to Archive Contents
3c160414da2e initial upload
shiltemann
parents:
diff changeset
719 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
720 if [[ ${myarr[1]} == "links" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
721 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
722 archive=${myarr[2]}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
723 decompressArchive $archive
3c160414da2e initial upload
shiltemann
parents:
diff changeset
724
3c160414da2e initial upload
shiltemann
parents:
diff changeset
725 # add links to webpage
3c160414da2e initial upload
shiltemann
parents:
diff changeset
726 # separate line for each folder, files within folder on same line
3c160414da2e initial upload
shiltemann
parents:
diff changeset
727 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
728 do
3c160414da2e initial upload
shiltemann
parents:
diff changeset
729 #echo "<br/> ->making link to file: $linkfile "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
730 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
3c160414da2e initial upload
shiltemann
parents:
diff changeset
731 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
732 #echo "<br/> ->is directory, entering: $linkfile "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
733 #ls ${galaxypath}/archive_${fname}/$linkfile
3c160414da2e initial upload
shiltemann
parents:
diff changeset
734 contentline="${contentline}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
735 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
736 do
3c160414da2e initial upload
shiltemann
parents:
diff changeset
737 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
738 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
3c160414da2e initial upload
shiltemann
parents:
diff changeset
739 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
740 #echo "<br/> ->is file, making link: $linkfile "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
741 label=`basename $linkfile2`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
742 label=${label%.*}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
743 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a>&nbsp;\n "
3c160414da2e initial upload
shiltemann
parents:
diff changeset
744 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
745 done
3c160414da2e initial upload
shiltemann
parents:
diff changeset
746 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
747 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
748 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
3c160414da2e initial upload
shiltemann
parents:
diff changeset
749 label=${label%.*}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
750 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a>&nbsp;\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
751 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
752 done
3c160414da2e initial upload
shiltemann
parents:
diff changeset
753
3c160414da2e initial upload
shiltemann
parents:
diff changeset
754
3c160414da2e initial upload
shiltemann
parents:
diff changeset
755 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
756
3c160414da2e initial upload
shiltemann
parents:
diff changeset
757 if [[ ${myarr[3]} == "Y" ]]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
758 then
3c160414da2e initial upload
shiltemann
parents:
diff changeset
759 contentline="${contentline}<br/>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
760 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
761 fi
3c160414da2e initial upload
shiltemann
parents:
diff changeset
762 done
3c160414da2e initial upload
shiltemann
parents:
diff changeset
763
3c160414da2e initial upload
shiltemann
parents:
diff changeset
764 echo "${contentline}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
765 }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
766
3c160414da2e initial upload
shiltemann
parents:
diff changeset
767 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
768 ## Create HTML content for iReport
3c160414da2e initial upload
shiltemann
parents:
diff changeset
769 ##
3c160414da2e initial upload
shiltemann
parents:
diff changeset
770 createMainPage (){
3c160414da2e initial upload
shiltemann
parents:
diff changeset
771 page=$1
3c160414da2e initial upload
shiltemann
parents:
diff changeset
772 tabtitles=$2 # comma-separated list of tab titles
3c160414da2e initial upload
shiltemann
parents:
diff changeset
773 tabitems=$3 # colon-sparated list of tabs specifications
3c160414da2e initial upload
shiltemann
parents:
diff changeset
774 iframecount=1 # keep track of number of iFrames so that they can be referenced by ID
3c160414da2e initial upload
shiltemann
parents:
diff changeset
775 minwidth=$4 # width of page
3c160414da2e initial upload
shiltemann
parents:
diff changeset
776 gbtracks=$5 # genome browser track information
3c160414da2e initial upload
shiltemann
parents:
diff changeset
777
3c160414da2e initial upload
shiltemann
parents:
diff changeset
778 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
779 # create correct number of tabs
3c160414da2e initial upload
shiltemann
parents:
diff changeset
780 count=0
3c160414da2e initial upload
shiltemann
parents:
diff changeset
781
3c160414da2e initial upload
shiltemann
parents:
diff changeset
782 tabtitles=${tabtitles//,/ }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
783 tabtitles=${tabtitles//==colon==/:}
3c160414da2e initial upload
shiltemann
parents:
diff changeset
784 tabslist="<ul>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
785 mytabs=""
3c160414da2e initial upload
shiltemann
parents:
diff changeset
786
3c160414da2e initial upload
shiltemann
parents:
diff changeset
787 for title in $tabtitles
3c160414da2e initial upload
shiltemann
parents:
diff changeset
788 do
3c160414da2e initial upload
shiltemann
parents:
diff changeset
789 # Create list of tabs
3c160414da2e initial upload
shiltemann
parents:
diff changeset
790 count=$[count+1]
3c160414da2e initial upload
shiltemann
parents:
diff changeset
791 title2=${title//_s_/ }
3c160414da2e initial upload
shiltemann
parents:
diff changeset
792 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
793
3c160414da2e initial upload
shiltemann
parents:
diff changeset
794 # Create tabs with content
3c160414da2e initial upload
shiltemann
parents:
diff changeset
795 tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks")
3c160414da2e initial upload
shiltemann
parents:
diff changeset
796 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
797 mytabs="${mytabs}${tabcontent}"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
798 mytabs="${mytabs}\n</div>\n"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
799 done
3c160414da2e initial upload
shiltemann
parents:
diff changeset
800 tabslist="${tabslist}</ul>"
3c160414da2e initial upload
shiltemann
parents:
diff changeset
801
3c160414da2e initial upload
shiltemann
parents:
diff changeset
802 ## Output the webpage
3c160414da2e initial upload
shiltemann
parents:
diff changeset
803 echo -e "<!doctype html>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
804 <head>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
805 <meta charset=\"utf-8\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
806 <title>iReport</title>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
807 <link rel=\"stylesheet\" href=\"jquery-ui.css\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
808 <link rel=\"stylesheet\" href=\"ireport_css.css\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
809 <link rel=\"stylesheet\" href=\"md.css\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
810 <script type=\"text/javascript\" src=\"jquery-1.10.2.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
811 <script type=\"text/javascript\" src=\"jquery-ui.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
812 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
813 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
814 <script type=\"text/javascript\" src=\"ireport_jquery.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
815 <script type=\"text/javascript\" src=\"ireport_javascript.js\"></script>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
816 </head>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
817 <body>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
818 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\">
3c160414da2e initial upload
shiltemann
parents:
diff changeset
819 $tabslist
3c160414da2e initial upload
shiltemann
parents:
diff changeset
820
3c160414da2e initial upload
shiltemann
parents:
diff changeset
821 $mytabs
3c160414da2e initial upload
shiltemann
parents:
diff changeset
822 </div>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
823 </body>
3c160414da2e initial upload
shiltemann
parents:
diff changeset
824 </html>" > $page
3c160414da2e initial upload
shiltemann
parents:
diff changeset
825 }