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1 #!/bin/bash
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2
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3
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4 echo "allparams: $@"
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5 function usage() { echo "Oops!"; }
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6
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7
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8 # set some defaults
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9
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10 gbcount=0
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11 set -- `getopt -n$0 -u -a --longoptions="ifusepath: galaxypath: tab: item: genomebrowsertrack: newgb: htmlout: label: toolpath: minwidth: coverimage:" "h:" "$@"` || usage
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12 [ $# -eq 0 ] && usage
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13
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14 while [ $# -gt 0 ]
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15 do
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16 case "$1" in
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17 --toolpath) repositorypath=$2;shift;;
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18 --galaxypath) galaxypath=$2;shift;;
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19 --minwidth) minwidth=$2;shift;;
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20 --tab) tabs+=",$2";shift;;
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21 --item) items+=",$2";shift;;
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22 --newgb) gbcount=$[$gbcount+1];shift;;
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23 --genomebrowsertrack) gbtracks+=",${gbcount}:$2";shift;;
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24 --htmlout) htmlout=$2;shift;;
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25 --label) title="$@";shift;;
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26 --coverimage) coverimage=$2;shift;;
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27 -h) shift;;
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28 --) shift;break;;
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29 -*) usage;;
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30 *) break;;
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31 esac
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32 shift
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33 done
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34
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35 source "${repositorypath}/createHTML.sh"
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36 mkdir $galaxypath
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37
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38 tabs=${tabs//,/ }; tabs=${tabs/ /}
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39 gbtracks=${gbtracks:1}
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40 items=${items//,/ }; items=${items/ /}
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41 echo -e "title: $title"
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42
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43 #title=${title%--*}
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44 title=${title//--/}
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45 title=${title//label/}
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46
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47 reportname=${title// /}
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48
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49 echo -e "\n"
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50 echo -e "title: $title"
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51 echo -e "tabs: $tabs"
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52 echo -e "items: $items"
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53 echo -e "htmlout: $htmlout"
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54 echo -e "coverimage: $coverimage"
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55 echo -e "gbtracks: ${gbtracks[@]}"
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56 echo -e "gbcount: ${gbcount}"
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57 echo -e "\n"
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58
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59 for i in $tabs
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60 do
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61 echo "tabname: $i"
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62 done
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63
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64 coverimage=${coverimage:1}
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65 echo -e "coverimage2: $coverimage"
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66
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67 #if no coverimage provided, use default EMC logo
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68 if [[ -z $coverimage ]]
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69 then
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70 cp $repositorypath/intro.jpg ${galaxypath}/intro.jpg
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71 coverimage="intro.jpg"
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72 fi
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73 echo -e "coverimage3: $coverimage"
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74
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75 ## Copy supporting files from repository to output directory
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76 cp ${repositorypath}/jquery.dataTables.css ${galaxypath}/jquery.dataTables.css
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77 cp ${repositorypath}/jquery.dataTables.js ${galaxypath}/jquery.dataTables.js
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78 cp -R ${repositorypath}/iframe-resizer/ ${galaxypath}/iframe-resizer/
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79 cp -R ${repositorypath}/DataTables-1.9.4/ ${galaxypath}/DataTables-1.9.4/
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80 cp ${repositorypath}/jquery.zoom.js ${galaxypath}/jquery.zoom.js
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81 cp ${repositorypath}/jquery-ui.css ${galaxypath}/jquery-ui.css
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82 cp ${repositorypath}/jquery-1.10.2.js ${galaxypath}/jquery-1.10.2.js
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83 cp ${repositorypath}/jquery-ui.js ${galaxypath}/jquery-ui.js
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84 cp ${repositorypath}/md.css ${galaxypath}/md.css
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85 cp ${repositorypath}/ireport_css.css ${galaxypath}/ireport_css.css
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86 cp ${repositorypath}/ireport_jquery.js ${galaxypath}/ireport_jquery.js
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87
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88 echo "done copying resource files"
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89 ls ${galaxypath}
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90
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91
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92 ## Create cover HTML page
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93 makeIntroPage "$title" $coverimage "report.html" $htmlout iReport_${reportname}.zip
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94
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95 ## Create copy of cover page for downloadable version
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96 makeIntroPage "$title" $coverimage "report.html" coverpage.html iReport_${reportname}.zip
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97 cp coverpage.html ${galaxypath}/coverpage.html
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98
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99 ## Create Report page with tabs
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100 createMainPage ${galaxypath}/report.html "$tabs" "$items" $minwidth "$gbtracks"
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101
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102
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103 ## Create zip file of this iReport for download by user
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104 wd=`pwd`
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105 cd ${galaxypath}
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106 zip -r iReport_${reportname} .
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107 cd $wd
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108
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109 wait |
