ireport: iReport.sh annotate

annotate iReport.sh @ 8:86219e4aa239 draft

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

rev	line source
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	1 #!/bin/bash
3 4a6ebda2a3ae fixed tool dependency issue saskia-hiltemann parents: 2 diff changeset	2
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	3
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	4 echo "allparams: $@"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	5 function usage() { echo "Oops!"; }
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	6
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	7
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	8 # set some defaults
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	9
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	10 gbcount=0
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	11 set -- `getopt -n$0 -u -a --longoptions="ifusepath: galaxypath: tab: item: genomebrowsertrack: newgb: htmlout: label: toolpath: minwidth: coverimage:" "h:" "$@"` \|\| usage
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	12 [ $# -eq 0 ] && usage
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	13
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	14 while [ $# -gt 0 ]
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	15 do
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	16 case "$1" in
2 e8755431a0cd fixed missing dependencies saskia-hiltemann parents: 1 diff changeset	17 --toolpath) repositorypath=$2;shift;;
e8755431a0cd fixed missing dependencies saskia-hiltemann parents: 1 diff changeset	18 --galaxypath) galaxypath=$2;shift;;
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	19 --minwidth) minwidth=$2;shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	20 --tab) tabs+=",$2";shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	21 --item) items+=",$2";shift;;
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	22 --newgb) gbcount=$[$gbcount+1];shift;;
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	23 --genomebrowsertrack) gbtracks+=",${gbcount}:$2";shift;;
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	24 --htmlout) htmlout=$2;shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	25 --label) title="$@";shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	26 --coverimage) coverimage=$2;shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	27 -h) shift;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	28 --) shift;break;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	29 -*) usage;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	30 *) break;;
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	31 esac
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	32 shift
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	33 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	34
3 4a6ebda2a3ae fixed tool dependency issue saskia-hiltemann parents: 2 diff changeset	35 source "${repositorypath}/createHTML.sh"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	36 mkdir $galaxypath
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	37
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	38 #tabs=${tabs//,/ }; tabs=${tabs/ /}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	39 #tabs=${tabs//==dollar==/$}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	40 #tabs=${tabs//==braceopen==/(}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	41 #tabs=${tabs//==braceclose==/)}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	42 gbtracks=${gbtracks:1}
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	43 items=${items//,/ }; items=${items/ /}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	44
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	45 title=${title//--/}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	46 title=${title//label/}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	47 title=${title// /}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	48
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	49 echo -e "title: $title"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	50 echo -n "$title" > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	51 title=`base64 -d tmpfileb64`
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	52 echo -e "title decoded: $title"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	53
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	54 #title=${title%--*}
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	55
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	56 reportname=${title// /}
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	57
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	58 echo -e "\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	59 echo -e "title: $title"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	60 echo -e "tabs: $tabs"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	61 echo -e "items: $items"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	62 echo -e "htmlout: $htmlout"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	63 echo -e "coverimage: $coverimage"
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	64 echo -e "gbtracks: ${gbtracks[@]}"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	65 echo -e "gbcount: ${gbcount}"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	66 echo -e "\n"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	67
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	68 for i in $tabs
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	69 do
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	70 echo "tabname: $i"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	71 done
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	72
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	73
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	74
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	75 #if no coverimage provided, use default EMC logo
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	76 if [[ $coverimage == "-" ]]
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	77 then
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	78 cp $repositorypath/intro.jpg ${galaxypath}/intro.jpg
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	79 coverimage="intro.jpg"
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	80 else
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	81 coverimage=${coverimage:1}
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	82 echo -n "$coverimage" > tmpfileb64
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	83 coverimage=`base64 -d tmpfileb64`
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	84 fi
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	85
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 3 diff changeset	86 ## Copy supporting files from repository to output directory
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	87 cp ${repositorypath}/jquery.dataTables.css ${galaxypath}/jquery.dataTables.css
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	88 cp ${repositorypath}/jquery.dataTables.js ${galaxypath}/jquery.dataTables.js
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	89 cp -R ${repositorypath}/iframe-resizer/ ${galaxypath}/iframe-resizer/ > /dev/null 2>&1
42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	90 cp -R ${repositorypath}/DataTables-1.9.4/ ${galaxypath}/DataTables-1.9.4/ > /dev/null 2>&1
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	91 cp ${repositorypath}/jquery.zoom.js ${galaxypath}/jquery.zoom.js
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	92 cp ${repositorypath}/jquery-ui.css ${galaxypath}/jquery-ui.css
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	93 cp ${repositorypath}/jquery-1.10.2.js ${galaxypath}/jquery-1.10.2.js
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	94 cp ${repositorypath}/jquery-ui.js ${galaxypath}/jquery-ui.js
4 a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 3 diff changeset	95 cp ${repositorypath}/md.css ${galaxypath}/md.css
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 3 diff changeset	96 cp ${repositorypath}/ireport_css.css ${galaxypath}/ireport_css.css
a4813532bbc6 Added MarkDown support saskia-hiltemann parents: 3 diff changeset	97 cp ${repositorypath}/ireport_jquery.js ${galaxypath}/ireport_jquery.js
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	98
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	99 echo "done copying resource files"
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	100 ls ${galaxypath}
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	101
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	102
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	103 ## Create cover HTML page
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	104 makeIntroPage "$title" $coverimage "report.html" $htmlout iReport_${reportname}.zip
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	105
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	106 ## Create copy of cover page for downloadable version
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	107 makeIntroPage "$title" $coverimage "report.html" coverpage.html iReport_${reportname}.zip
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	108 cp coverpage.html ${galaxypath}/coverpage.html
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	109
ac5f9272033b first upload saskia-hiltemann parents: diff changeset	110 ## Create Report page with tabs
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	111 createMainPage ${galaxypath}/report.html "$tabs" "$items" $minwidth "$gbtracks"
0 ac5f9272033b first upload saskia-hiltemann parents: diff changeset	112
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	113
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	114 ## Create zip file of this iReport for download by user
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	115 wd=`pwd`
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	116 cd ${galaxypath}
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	117 zip -r iReport_${reportname} . > /dev/null 2>&1
1 440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	118 cd $wd
440f4aa3db97 Added option to dowload iReports saskia-hiltemann parents: 0 diff changeset	119
6 42076db43d42 Fixed auto resizing plus various other minor bugs saskia-hiltemann parents: 4 diff changeset	120 wait

Mercurial > repos > saskia-hiltemann > ireport

annotate iReport.sh @ 8:86219e4aa239 draft