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2
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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==/<}
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211 text=${text//==gt==/>}
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212 text=${text//==apos==/'}
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213 text=${text//==quote==/"}
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214 text=${text//&&/&}
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215 text=${text//\\n/<br/>}
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216 text=${text//\\t/ }
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217 text=${text//\&r\&n/<br/>}
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218 text=${text//\&r/<br/>}
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219 text=${text//\&n/<br/>}
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220 text=${text//\&c/:}
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221 text=${text//==backtick==/`}
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222 text=${text//==dollar==/$}
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223 text=${text//==bar==/|}
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224 contentline="${contentline}\n${text}\n"
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225 fi
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226
|
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227
|
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228 fi
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229
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230 ##
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231 ## Text File
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232 ##
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233 if [ ${myarr[1]} == "textfile" ]
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234 then
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235 tfile=${myarr[2]}
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236 md=${myarr[4]}
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237 fname=`basename ${tfile}`
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238 fname=${fname%.*}
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239 fname="${fname}.txt"
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240 cp ${tfile} "${galaxypath}/${fname}"
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241
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242 #estimate height for iframe based on number oflines in the file
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243 numlines=`wc -l ${tfile} | cut -d" " -f1`
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244 minheight=$[$numlines*17]
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245
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246 # if markdown, convert to html
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247 if [ $md == "Y" ]
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248 then
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249
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250 if [ -z `type -p pandoc` ]
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251 then
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252 # pandoc missing
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253 ${repositorypath}/Markdown/markdown2.py ${tfile} > mytext.html
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254
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255 else
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256 # pandoc exists
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257 pandoc -o mytext.html ${tfile}
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258 pandoc -o standalone.html -s ${tfile}
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259
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260 # get css generated by pandoc and add as scoped attribute (HTML5)
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261 pandocstyle=`sed -n '/<style/,/style>/p' standalone.html`
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262
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263 fi
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264
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265 markdowntext=$(cat mytext.html)
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266 contentline="${contentline}\n<div class=\"markdown-body\">${pandocstyle} ${markdowntext}</div>\n"
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267 else
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268 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${fname}\" width=\"100%\" height=\"$minheight\"> </iframe>\n"
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269 fi
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270 fi
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271
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272 ##
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273 ## Image
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274 ##
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275 if [ ${myarr[1]} == "image" ]
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276
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277 then
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278 imgcount=$[$imgcount+1]
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279 #restore file suffix for html
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280 ftype=`file ${myarr[2]}`
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281 zoomlevel=${myarr[4]}
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282 zoomenable=${myarr[5]}
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283 align=${myarr[6]}
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284 #####echo "zoomenable:${zoomenable}, align:${align}"
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285 if [[ $ftype == *JPEG* ]]
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286 then
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287 suffix=".jpg"
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288 fi
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289 if [[ $ftype == *SVG* ]]
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290 then
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291 suffix=".svg"
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292 fi
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293 if [[ $ftype == *PNG* ]]
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294 then
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295 suffix=".png"
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296 fi
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297
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298 image=`basename ${myarr[2]}`
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299 image=${image%.dat}
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300 image="${image}${suffix}"
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301 cp ${myarr[2]} ${galaxypath}/${image}
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302
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303 if [[ ${align} == "none" ]]
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304 then
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305 alignstring=""
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306 alignstring2=""
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307 else
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308 alignstring="<div float=\"${align}\">"
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309 alignstring2="</div>"
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310
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311 alignstring="align=\"${align}\""
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312 alignstring2=""
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313 fi
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314
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315
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316 if [[ ${zoomlevel} -eq 0 ]]
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317 then
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318 widthstring=""
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319 else
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320 widthstring="width=\"${zoomlevel}\""
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321 fi
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322
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323 if [[ ${zoomlevel} -eq 0 || ${zoomenable} == "N" ]]
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324 then
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325 contentline="${contentline}<span id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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326 else
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327 contentline="${contentline}<span class=\"zoomme\" id=\"img${imgcount}\"> <img src=\"${image}\" ${alignstring} ${widthstring} alt=\"loading image..\"/></span>"
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|
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328 fi
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329
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330 fi
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331
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332 ##
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333 ## Table
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|
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334 ##
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335 if [ ${myarr[1]} == "table" ]
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336 then
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337
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338 maxlines=50000
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339 tsvfile_orig=${myarr[2]}
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|
340 tsvfile="tablehead.tsv"
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|
341 fname=`basename ${tsvfile_orig}`
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|
342 fname=${fname%.*}
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|
343 fancy=${myarr[4]}
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|
344 makelinks=${myarr[5]}
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|
|
345 iframeid="iframe"$iframecount
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|
346 #echo "\nmakelinks: $makelinks fancy: $fancy <br>"
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347
|
|
|
348 #TODO client side database for large files. For now only display first section of file and add download link
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|
|
349 numlines=`wc -l ${tsvfile_orig} |cut -d" " -f1`
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350
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|
351 head -${maxlines} ${tsvfile_orig} > tsvtmpfile
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352
|
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|
353 #remove any empty or header lines (lines starting with #, unless vcf file, then keep #CHROM line)
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|
|
354 awk 'BEGIN{
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355 FS="\t"
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356 OFS="\t"
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357 }{
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|
358 if((index($0,"#")==1 && index($0,"#CHROM")!=1) || $0==""){
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|
|
359 headerlines++
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|
|
360 }
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|
|
361 else print $0
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|
|
362
|
|
|
363 }END{}' tsvtmpfile > ${tsvfile}
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|
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364
|
|
|
365 if [[ $makelinks == "Y" ]]
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|
366 then
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|
367 col=${myarr[6]}
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368 prefix=${myarr[7]}
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|
|
369 suffix=${myarr[8]}
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|
370 urlitems=${myarr[9]}
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371 minw=${myarr[10]}
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|
372 suffix=${suffix/emptycol/}
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|
373 suffix=${suffix/==quote==/&}
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|
|
374 prefix=${prefix/emptycol/}
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|
|
375 prefix=${prefix/==quote==/&}
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|
376 prefix=${prefix/==colon==/:}
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|
|
377
|
|
|
378 # unpack archive of files to link to if present
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|
|
379 if [[ ${urlitems} != None ]]
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|
|
380 then
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|
|
381 oldfname=$fname
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|
|
382 decompressArchive ${urlitems}
|
|
|
383 prefix=archive_${fname}/${prefix}
|
|
|
384 fname=$oldfname
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|
|
385 fi
|
|
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386
|
|
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387
|
|
|
388 #edit the table to include links
|
|
|
389 awk 'BEGIN{
|
|
|
390 FS="\t"
|
|
|
391 OFS="\t"
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|
|
392 url="'"$prefix"'"
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|
|
393 url2="'"$suffix"'"
|
|
|
394 iframeid="'"$iframeid"'"
|
|
|
395 prefix="<a href=\42"
|
|
|
396 suffix="\42 onclick=\42resizeIframe("iframeid")\42>"
|
|
|
397 col="'"$col"'"
|
|
|
398 end="</a>"
|
|
|
399 }{
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|
|
400 if(FNR==1)
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|
|
401 print $0
|
|
|
402 else{
|
|
|
403 $col=prefix""url""$col""url2""suffix""$col""end
|
|
|
404 print $0
|
|
|
405 }
|
|
|
406 }END{}' ${tsvfile} > ${tsvfile}2
|
|
|
407
|
|
|
408 else
|
|
|
409 minw=${myarr[6]}
|
|
|
410 cp ${tsvfile} ${tsvfile}2
|
|
|
411 fi
|
|
|
412
|
|
|
413 iframecount=$[$iframecount+1]
|
|
|
414 if [ $fancy == "Y" ]
|
|
|
415 then
|
|
|
416 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
|
|
|
417 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 760px; min-height: 525px; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
|
|
|
418 iframecount=$[$iframecount+1]
|
|
|
419 else
|
|
|
420 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
|
|
|
421 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
|
|
|
422 iframecount=$[$iframecount+1]
|
|
|
423 fi
|
|
|
424
|
|
|
425 if [[ $numlines -gt ${maxlines} ]]
|
|
|
426 then
|
|
|
427 tablename=`basename ${tsvfile_orig}`
|
|
|
428 cp ${tsvfile_orig} ${galaxypath}/$tablename
|
|
|
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>."
|
|
|
430 fi
|
|
|
431 fi
|
|
|
432
|
|
|
433 ##
|
|
|
434 ## PDF
|
|
|
435 ##
|
|
|
436 if [[ ${myarr[1]} == "pdf" ]]
|
|
|
437 then
|
|
|
438 pdffile=${myarr[2]}
|
|
|
439 fname=`basename ${pdffile}`
|
|
|
440 fname=${fname%.dat}
|
|
|
441 pdfname="${fname}.pdf"
|
|
|
442 cp ${pdffile} "${galaxypath}/${pdfname}"
|
|
|
443
|
|
|
444 width=1000
|
|
|
445 height=800
|
|
|
446 echo -e "<html><body><object data=\"${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"
|
|
|
447 width=$[$width+10]
|
|
|
448 height=$[$height+10]
|
|
|
449 contentline="${contentline}\n<iframe src=\"${fname}.html\" width=\"${width}\" height=\"${height}\"></iframe>\n"
|
|
|
450
|
|
|
451 fi
|
|
|
452
|
|
|
453 ##
|
|
|
454 ## HTML
|
|
|
455 ##
|
|
|
456 if [[ ${myarr[1]} == "htmlfile" ]]
|
|
|
457 then
|
|
|
458 htmlfile=${myarr[2]}
|
|
|
459 height=${myarr[4]}
|
|
|
460 fname=`basename ${htmlfile}`
|
|
|
461 fname=${fname%.dat}
|
|
|
462 htmlname="${fname}.html"
|
|
|
463 cp ${htmlfile} "${galaxypath}/${htmlname}"
|
|
|
464
|
|
|
465 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${htmlname}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
|
|
|
466 fi
|
|
|
467
|
|
|
468
|
|
|
469 if [[ ${myarr[1]} == "htmlpage" ]]
|
|
|
470 then
|
|
|
471 url=${myarr[2]}
|
|
|
472 url=${url//==colon==/:}
|
|
|
473 url=${url//==fslash==//}
|
|
|
474 height=${myarr[4]}
|
|
|
475
|
|
|
476 contentline="${contentline}\n<iframe class=\"invisibleframe\" src=\"${url}\" width=\"100%\" height=\"${height}px\"></iframe>\n"
|
|
|
477 fi
|
|
|
478
|
|
|
479 ##
|
|
|
480 ## Web Link
|
|
|
481 ##
|
|
|
482 if [ ${myarr[1]} == "weblink" ]
|
|
|
483 then
|
|
|
484 url=${myarr[2]}
|
|
|
485 linktext=${myarr[4]}
|
|
|
486 url=${url/==colon==/:}
|
|
|
487 url=${url/==quote==/&}
|
|
|
488
|
|
|
489 contentline="${contentline}<a href=\"${url}\" target=\"_blank\">${linktext}</a>"
|
|
|
490 fi
|
|
|
491
|
|
|
492
|
|
|
493 ##
|
|
|
494 ## Genome Browser
|
|
|
495 ##
|
|
|
496 if [ ${myarr[1]} == "genomebrowser" ]
|
|
|
497 then
|
|
|
498 # parse inputs
|
|
|
499
|
|
|
500 apiid=${myarr[4]}
|
|
|
501 servername=${myarr[5]}
|
|
|
502 buildver=${myarr[2]}
|
|
|
503
|
|
|
504 #TODO
|
|
|
505 ftype="vcf"
|
|
|
506
|
|
|
507 servername=${servername/==colon==/:}
|
|
|
508
|
|
|
509 ## parse and prepare all tracks
|
|
|
510 gbcount=$[$gbcount+1]
|
|
|
511 gbfilelist=${tracklist}
|
|
|
512 userTracks=""
|
|
|
513 #IFS=',' read -a gbfilearray <<< ${gbfilelist}
|
|
|
514 gbfilearray=(${gbfilelist//,/ })
|
|
|
515 for gbfile in "${gbfilearray[@]}"
|
|
|
516 do
|
|
|
517 # gbfile is in format "browsernum:file"
|
|
|
518 #IFS=':' read -a gbfileinfo <<< ${gbfile}
|
|
|
519 gbfileinfo=(${gbfile//:/ })
|
|
|
520 if [[ ${gbfileinfo[0]} == $gbcount ]]
|
|
|
521 then
|
|
|
522
|
|
|
523 ftype=${gbfileinfo[3]}
|
|
|
524 if [ $ftype == "vcf" ]
|
|
|
525 then
|
|
|
526 gbfilename=${gbfileinfo[1]}
|
|
|
527 gbfilelabel=${gbfileinfo[2]}
|
|
|
528 gbfilelabel=${gbfilelabel//==space==/ }
|
|
|
529 fname=`basename ${gbfilename}`
|
|
|
530 fname=${fname%.dat}
|
|
|
531 newgbfilename="${fname}.vcf"
|
|
|
532
|
|
|
533
|
|
|
534 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
|
|
|
535 bgzip "${galaxypath}/${newgbfilename}"
|
|
|
536 tabix -p vcf "${galaxypath}/${newgbfilename}.gz"
|
|
|
537
|
|
|
538 userTracks="${userTracks},
|
|
|
539 {name: '${gbfilelabel}',
|
|
|
540 uri: '${servername}/datasets/${apiid}/display/${newgbfilename}.gz',
|
|
|
541 tier_type: 'tabix',
|
|
|
542 payload: 'vcf'}
|
|
|
543 "
|
|
|
544 fi
|
|
|
545
|
|
|
546 if [ $ftype == "bam" ]
|
|
|
547 then
|
|
|
548 gbfilename=${gbfileinfo[1]}
|
|
|
549 gbfilelabel=${gbfileinfo[2]}
|
|
|
550 gbfilelabel=${gbfilelabel//==space==/ }
|
|
|
551 fname=`basename ${gbfilename}`
|
|
|
552 fname=${fname%.dat}
|
|
|
553 newgbfilename="${fname}.bam"
|
|
|
554
|
|
|
555 # link to bam instead of copying
|
|
|
556 ln -s ${gbfilename} "${galaxypath}/${newgbfilename}"
|
|
|
557 samtools index "${galaxypath}/${newgbfilename}"
|
|
|
558
|
|
|
559 userTracks="${userTracks},
|
|
|
560 {name: '${gbfilelabel}',
|
|
|
561 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
|
|
|
562 "
|
|
|
563
|
|
|
564 fi
|
|
|
565 fi
|
|
|
566 done
|
|
|
567
|
|
|
568
|
|
|
569
|
|
|
570 if [ ${buildver} == "hg18" ]
|
|
|
571 then
|
|
|
572 coordSystem="coordSystem: {
|
|
|
573 speciesName: 'Human',
|
|
|
574 taxon: 9606,
|
|
|
575 auth: 'NCBI',
|
|
|
576 version: '36',
|
|
|
577 ucscName: 'hg18'
|
|
|
578 },"
|
|
|
579
|
|
|
580 chains="chains: {
|
|
|
581 hg19ToHg18: new Chainset('https://www.biodalliance.org/das/hg19ToHg18/', 'GRCh37', 'NCBI36',
|
|
|
582 {
|
|
|
583 speciesName: 'Human',
|
|
|
584 taxon: 9606,
|
|
|
585 auth: 'GRCh',
|
|
|
586 version: 37
|
|
|
587 })
|
|
|
588 },"
|
|
|
589
|
|
|
590 genesTrack="{name: 'Genes',
|
|
|
591 desc: 'Gene structures from Ensembl 54',
|
|
|
592 uri: 'https://www.biodalliance.org/das/hsa_54_36p/',
|
|
|
593 collapseSuperGroups: true,
|
|
|
594 provides_karyotype: true,
|
|
|
595 provides_search: true,
|
|
|
596 provides_entrypoints: true,
|
|
|
597 maxbins: false}, "
|
|
|
598
|
|
|
599 repeatsTrack="{name: 'Repeats',
|
|
|
600 desc: 'Repeat annotation from Ensembl 59',
|
|
|
601 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
|
|
|
602 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'}"
|
|
|
603
|
|
|
604
|
|
|
605 # default is hg19
|
|
|
606 else
|
|
|
607 coordSystem="coordSystem: {
|
|
|
608 speciesName: 'Human',
|
|
|
609 taxon: 9606,
|
|
|
610 auth: 'NCBI',
|
|
|
611 version: '37',
|
|
|
612 ucscName: 'hg19'
|
|
|
613 },"
|
|
|
614
|
|
|
615 chains=""
|
|
|
616
|
|
|
617 genesTrack="{name: 'Genes',
|
|
|
618 desc: 'Gene structures from GENCODE 19',
|
|
|
619 bwgURI: 'https://www.biodalliance.org/datasets/gencode.bb',
|
|
|
620 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml',
|
|
|
621 collapseSuperGroups: true,
|
|
|
622 trixURI: 'https://www.biodalliance.org/datasets/geneIndex.ix'},"
|
|
|
623
|
|
|
624 repeatsTrack="{name: 'Repeats',
|
|
|
625 desc: 'Repeat annotation from Ensembl 59',
|
|
|
626 bwgURI: 'https://www.biodalliance.org/datasets/repeats.bb',
|
|
|
627 stylesheet_uri: 'https://www.biodalliance.org/stylesheets/bb-repeats.xml'},"
|
|
|
628
|
|
|
629 fi
|
|
|
630
|
|
|
631 contentline="${contentline}
|
|
|
632 <script language=\"javascript\" src=\"https://www.biodalliance.org/release-0.13/dalliance-compiled.js\"></script>
|
|
|
633 <script language=\"javascript\">
|
|
|
634 new Browser({
|
|
|
635 chr: '1',
|
|
|
636 viewStart: 0,
|
|
|
637 viewEnd: 100000,
|
|
|
638 cookieKey: 'human',
|
|
|
639
|
|
|
640 ${coordSystem}
|
|
|
641
|
|
|
642 ${chains}
|
|
|
643 sources: [{name: 'Genome',
|
|
|
644 twoBitURI: 'https://www.biodalliance.org/datasets/${buildver}.2bit',
|
|
|
645 tier_type: 'sequence'},
|
|
|
646 ${genesTrack},
|
|
|
647 ${repeatsTrack},
|
|
|
648 {name: 'Conservation',
|
|
|
649 desc: 'Conservation',
|
|
|
650 bwgURI: 'https://www.biodalliance.org/datasets/phastCons46way.bw',
|
|
|
651 noDownsample: true}
|
|
|
652 ${userTracks}
|
|
|
653 ],
|
|
|
654
|
|
|
655
|
|
|
656
|
|
|
657
|
|
|
658 browserLinks: {
|
|
|
659 Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
|
|
|
660 UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=${buildver}&position=chr${chr}:${start}-${end}',
|
|
|
661 Sequence: 'http://www.derkholm.net:8080/das/${buildver}comp/sequence?segment=${chr}:${start},${end}'
|
|
|
662 }
|
|
|
663
|
|
|
664 });
|
|
|
665 </script>
|
|
|
666
|
|
|
667 <div id=\"svgHolder\"></div>
|
|
|
668 "
|
|
|
669 fi
|
|
|
670
|
|
|
671 ##
|
|
|
672 ## Link to Dataset
|
|
|
673 ##
|
|
|
674 if [ ${myarr[1]} == "link" ]
|
|
|
675 then
|
|
|
676 linkfile=${myarr[2]}
|
|
|
677 apiid=${myarr[4]}
|
|
|
678 isireport=${myarr[5]}
|
|
|
679 linkfilename=`basename ${linkfile}`
|
|
|
680 linktext=${myarr[6]}
|
|
|
681
|
|
|
682
|
|
|
683 #check for some basic filetypes
|
|
|
684 ftype=`file $linkfile`
|
|
|
685 if [[ $ftype == *HTML* ]]
|
|
|
686 then
|
|
|
687 linkfilename=${linkfilename%.dat}
|
|
|
688 linkfilename=${linkfilename}.html
|
|
|
689 fi
|
|
|
690 if [[ $ftype == *PNG* ]]
|
|
|
691 then
|
|
|
692 linkfilename=${linkfilename%.dat}
|
|
|
693 linkfilename=${linkfilename}.png
|
|
|
694 fi
|
|
|
695 if [[ $ftype == *SVG* ]]
|
|
|
696 then
|
|
|
697 linkfilename=${linkfilename%.dat}
|
|
|
698 linkfilename=${linkfilename}.svg
|
|
|
699 fi
|
|
|
700 if [[ $ftype == *JPEG* ]]
|
|
|
701 then
|
|
|
702 linkfilename=${linkfilename%.dat}
|
|
|
703 linkfilename=${linkfilename}.jpg
|
|
|
704 fi
|
|
|
705
|
|
|
706
|
|
|
707 if [[ ${isireport} == "Y" ]]
|
|
|
708 then
|
|
|
709 linkfilename="/datasets/${apiid}/display/"
|
|
|
710 else
|
|
|
711 cp ${linkfile} "${galaxypath}/${linkfilename}"
|
|
|
712 fi
|
|
|
713
|
|
|
714 contentline="${contentline}<a href=\"${linkfilename}\">${linktext}</a>"
|
|
|
715 fi
|
|
|
716
|
|
|
717 ##
|
|
|
718 ## Links to Archive Contents
|
|
|
719 ##
|
|
|
720 if [[ ${myarr[1]} == "links" ]]
|
|
|
721 then
|
|
|
722 archive=${myarr[2]}
|
|
|
723 decompressArchive $archive
|
|
|
724
|
|
|
725 # add links to webpage
|
|
|
726 # separate line for each folder, files within folder on same line
|
|
|
727 for linkfile in `ls ${galaxypath}/archive_${fname}/ |sort -V`
|
|
|
728 do
|
|
|
729 #echo "<br/> ->making link to file: $linkfile "
|
|
|
730 if [ -d ${galaxypath}/archive_${fname}/$linkfile ] # if directory, add break, and list all contained files, max level 1 deep
|
|
|
731 then
|
|
|
732 #echo "<br/> ->is directory, entering: $linkfile "
|
|
|
733 #ls ${galaxypath}/archive_${fname}/$linkfile
|
|
|
734 contentline="${contentline}"
|
|
|
735 for linkfile2 in `ls ${galaxypath}/archive_${fname}/$linkfile | sort -V`
|
|
|
736 do
|
|
|
737 #echo "<br/> ->making link to file: ${galaxypath}/archive_${fname}/$linkfile2"
|
|
|
738 if [ -f ${galaxypath}/archive_${fname}/$linkfile/$linkfile2 ] # if directory, add break, and list all contained files, max level 1 deep
|
|
|
739 then
|
|
|
740 #echo "<br/> ->is file, making link: $linkfile "
|
|
|
741 label=`basename $linkfile2`
|
|
|
742 label=${label%.*}
|
|
|
743 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}/${linkfile2}\">${label}</a> \n "
|
|
|
744 fi
|
|
|
745 done
|
|
|
746 elif [ -f ${galaxypath}/archive_${fname}/$linkfile ]
|
|
|
747 then
|
|
|
748 label=`basename ${galaxypath}/archive_${fname}/$linkfile`
|
|
|
749 label=${label%.*}
|
|
|
750 contentline="${contentline}<a class=\"mylinks\" href=\"archive_${fname}/${linkfile}\">$label</a> \n"
|
|
|
751 fi
|
|
|
752 done
|
|
|
753
|
|
|
754
|
|
|
755 fi
|
|
|
756
|
|
|
757 if [[ ${myarr[3]} == "Y" ]]
|
|
|
758 then
|
|
|
759 contentline="${contentline}<br/>\n"
|
|
|
760 fi
|
|
|
761 fi
|
|
|
762 done
|
|
|
763
|
|
|
764 echo "${contentline}"
|
|
|
765 }
|
|
|
766
|
|
|
767 ##
|
|
|
768 ## Create HTML content for iReport
|
|
|
769 ##
|
|
|
770 createMainPage (){
|
|
|
771 page=$1
|
|
|
772 tabtitles=$2 # comma-separated list of tab titles
|
|
|
773 tabitems=$3 # colon-sparated list of tabs specifications
|
|
|
774 iframecount=1 # keep track of number of iFrames so that they can be referenced by ID
|
|
|
775 minwidth=$4 # width of page
|
|
|
776 gbtracks=$5 # genome browser track information
|
|
|
777
|
|
|
778 echo "createMainPage: tabitems: $tabitems. tabtitles: $tabtitles. gbtracks: $gbtracks"
|
|
|
779 # create correct number of tabs
|
|
|
780 count=0
|
|
|
781
|
|
|
782 tabtitles=${tabtitles//,/ }
|
|
|
783 tabtitles=${tabtitles//==colon==/:}
|
|
|
784 tabslist="<ul>\n"
|
|
|
785 mytabs=""
|
|
|
786
|
|
|
787 for title in $tabtitles
|
|
|
788 do
|
|
|
789 # Create list of tabs
|
|
|
790 count=$[count+1]
|
|
|
791 title2=${title//_s_/ }
|
|
|
792 tabslist="${tabslist} <li><a href=\"#tabs-${count}\">${title2}</a></li>\n"
|
|
|
793
|
|
|
794 # Create tabs with content
|
|
|
795 tabcontent=$(makeTabContent $title "$tabitems" "$gbtracks")
|
|
|
796 mytabs="${mytabs}\n<div id=\"tabs-${count}\">\n"
|
|
|
797 mytabs="${mytabs}${tabcontent}"
|
|
|
798 mytabs="${mytabs}\n</div>\n"
|
|
|
799 done
|
|
|
800 tabslist="${tabslist}</ul>"
|
|
|
801
|
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802 ## Output the webpage
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803 echo -e "<!doctype html>
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804 <head>
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805 <meta charset=\"utf-8\">
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806 <title>iReport</title>
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807 <link rel=\"stylesheet\" href=\"jquery-ui.css\">
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808 <link rel=\"stylesheet\" href=\"ireport_css.css\">
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809 <link rel=\"stylesheet\" href=\"md.css\">
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810 <script type=\"text/javascript\" src=\"jquery-1.10.2.js\"></script>
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811 <script type=\"text/javascript\" src=\"jquery-ui.js\"></script>
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812 <script type=\"text/javascript\" src=\"iframe-resizer/src/iframeResizer.js\"></script>
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813 <script type=\"text/javascript\" src=\"jquery.zoom.js\"></script>
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814 <script type=\"text/javascript\" src=\"ireport_jquery.js\"></script>
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815 <script type=\"text/javascript\" src=\"ireport_javascript.js\"></script>
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816 </head>
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817 <body>
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818 <div id=\"tabs\" style=\"display:inline-block; min-height:100%; min-width:${minwidth}px\">
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819 $tabslist
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820
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821 $mytabs
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822 </div>
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823 </body>
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824 </html>" > $page
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825 }
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