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