debian/README.source

+multiqc for Debian
+-----------------
+
+Removing
+  .eggs folder since that is modified during build.
+
+and a series of files redundent with what is already in Debian, substituted
+with respective symbolic lincs
+  multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
+  multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
+  multiqc/templates/default/assets/js/packages/jquery-ui.min.js
+  multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
+  
+
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 22 Mar 2019 18:40:49 +0100
+

debian/changelog

-multiqc (1.7-1) UNRELEASED; urgency=medium
+multiqc (1.7+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #925304)
 

debian/control

 Source: multiqc
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille@debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+ Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
@@ -36,13 +37,29 @@ Depends: ${python3:Depends},
          python3-requests,
          python3-simplejson,
          python3-spectra
-Description: aggregate results from bioinformatics analyses across many samples into a single report
- MultiQC is a tool to create a single report with interactive plots for
- multiple bioinformatics analyses across many samples.
+Recommends:
+         fonts-glewlwyd,
+         libjs-jquery,
+         libjs-jquery-tablesorter,
+         libjs-jquery-ui
+Description: output integration for RNA sequencing across tools and samples
+ The sequencing of DNA or RNA with current high-throughput technologies
+ involves an array of tools and these are applied over a range of samples.
+ It is easy to loose oversight. And gathering the data and forwarding
+ them in a readable manner to the individuals who took the samples is
+ a challenge for a tool in itself. Well. Here it is.
+ MultiQC aggregates the output of multiple tools into a single report.
  .
  Reports are generated by scanning given directories for recognised log
- files. These are parsed and a single HTML report is generated
- summarising the statistics for all logs found. MultiQC reports can
- describe multiple analysis steps and large numbers of samples within a
- single plot, and multiple analysis tools making it ideal for routine
- fast quality control.
+ files. These are parsed and a single HTML report is generated summarising
+ the statistics for all logs found. MultiQC reports can describe multiple
+ analysis steps and large numbers of samples within a single plot, and
+ multiple analysis tools making it ideal for routine fast quality control.
+
+#  Needs more love
+#Package: python-multiqc-doc
+#Architecture: all
+#Section: doc
+#Depends: ${sphinxdoc:Depends}, ${misc:Depends}
+#Description: MultiQC biological sequencing QA (common documentation)
+# Markdown documentation for MultiQC.

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: multiqc
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
-           scan-copyrights
-         **** available in cme + lib-config-model-dpkg-perl     ****
-         **** package a try.  For existing copyright files try  ****
-           cme update dpkg-copyright
+Upstream-Name: MultiQC
+Source: https://github.com/ewels/MultiQC/
+Files-Excluded: .eggs
+ multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
+ multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
+ multiqc/templates/default/assets/js/packages/jquery-ui.min.js
+ multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
+# ./multiqc/templates/default/assets/js/packages/jquery.toast.min.js - not in Debian
 
 Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: Philip Ewels <phil.ewels@scilifelab.se>
+License: GPL-3.0+
 
 Files: debian/*
-Copyright: 2019 Andreas Tille <tille@debian.org>
-License: <license>
+Copyright: 2019 Andreas Tille <tilla@debian.org>
+                Steffen Moeller <moeller@debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

debian/multiqc-doc.docs

+docs

debian/multiqc-docs.docs

+README.Debian
+README.source

debian/multiqc.docs

+debian/README.source

debian/multiqc.links

+/usr/share/fonts/truetype/glyphicons/glyphicons-halflings-regular.ttf /usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
+/usr/share/javascript/jquery-ui/jquery.min.js /usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
+/usr/share/javascript/jquery-ui/jquery-ui.min.js /usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-ui.min.js
+/usr/share/javascript/jquery-tablesorter/jquery.tablesorter.min.js /usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js

debian/rules

@@ -27,3 +27,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cp -a $(PYBUILD_NAME)*.egg-info $(shell pybuild --print build_dir --interpreter python3)
 	dh_auto_test
 endif
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf multiqc.egg-info/

debian/source/lintian-overrides

+multiqc source: source-is-missing multiqc/modules/fastqc/assets/js/multiqc_fastqc.js line length is 281 characters (>256)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/multiqc_plotting.js line length is 1130 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/multiqc_toolbox.js line length is 339 characters (>256)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/FileSaver.min.js
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/bootstrap.min.js
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/clipboard.min.js
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/highcharts.export-csv.js line length is 4609 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/highcharts.exporting.js line length is 516 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/highcharts.heatmap.js line length is 519 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/highcharts.js line length is 519 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/highcharts.offline-exporting.js line length is 595 characters (>512)
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/jquery.toast.min.js
+multiqc source: source-is-missing multiqc/templates/default/assets/js/packages/lz-string.min.js

debian/upstream/metadata

@@ -10,3 +10,8 @@ Reference:
   PMID: 27312411
   URL: https://academic.oup.com/bioinformatics/article/32/19/3047/2196507
   eprint: https://academic.oup.com/bioinformatics/article-pdf/32/19/3047/25072524/btw354.pdf
+Registry:
+  - Name: OMICtools
+    Entry: NA
+  - Name: bio.tools
+    Entry: multiqc

debian/watch

 version=4
-
-https://github.com/ewels/MultiQC/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
+opts="repack,oversionmangle=s/$/+dfsg/,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%multiqc-$1.tar.gz%" \
+   https://github.com/ewels/multiqc/tags \
+   (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
+#https://github.com/ewels/MultiQC/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@

multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js

-
-(function($){$.extend({tablesorter:new
-function(){var parsers=[],widgets=[];this.defaults={cssHeader:"header",cssAsc:"headerSortUp",cssDesc:"headerSortDown",cssChildRow:"expand-child",sortInitialOrder:"asc",sortMultiSortKey:"shiftKey",sortForce:null,sortAppend:null,sortLocaleCompare:true,textExtraction:"simple",parsers:{},widgets:[],widgetZebra:{css:["even","odd"]},headers:{},widthFixed:false,cancelSelection:true,sortList:[],headerList:[],dateFormat:"us",decimal:'/\.|\,/g',onRenderHeader:null,selectorHeaders:'thead th',debug:false};function benchmark(s,d){log(s+","+(new Date().getTime()-d.getTime())+"ms");}this.benchmark=benchmark;function log(s){if(typeof console!="undefined"&&typeof console.debug!="undefined"){console.log(s);}else{alert(s);}}function buildParserCache(table,$headers){if(table.config.debug){var parsersDebug="";}if(table.tBodies.length==0)return;var rows=table.tBodies[0].rows;if(rows[0]){var list=[],cells=rows[0].cells,l=cells.length;for(var i=0;i<l;i++){var p=false;if($.metadata&&($($headers[i]).metadata()&&$($headers[i]).metadata().sorter)){p=getParserById($($headers[i]).metadata().sorter);}else if((table.config.headers[i]&&table.config.headers[i].sorter)){p=getParserById(table.config.headers[i].sorter);}if(!p){p=detectParserForColumn(table,rows,-1,i);}if(table.config.debug){parsersDebug+="column:"+i+" parser:"+p.id+"\n";}list.push(p);}}if(table.config.debug){log(parsersDebug);}return list;};function detectParserForColumn(table,rows,rowIndex,cellIndex){var l=parsers.length,node=false,nodeValue=false,keepLooking=true;while(nodeValue==''&&keepLooking){rowIndex++;if(rows[rowIndex]){node=getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex);nodeValue=trimAndGetNodeText(table.config,node);if(table.config.debug){log('Checking if value was empty on row:'+rowIndex);}}else{keepLooking=false;}}for(var i=1;i<l;i++){if(parsers[i].is(nodeValue,table,node)){return parsers[i];}}return parsers[0];}function 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$th=$(this).addClass(table.config.cssHeader);if(table.config.onRenderHeader)table.config.onRenderHeader.apply($th);}table.config.headerList[index]=this;});if(table.config.debug){benchmark("Built headers:",time);log($tableHeaders);}return $tableHeaders;};function computeTableHeaderCellIndexes(t){var matrix=[];var lookup={};var thead=t.getElementsByTagName('THEAD')[0];var trs=thead.getElementsByTagName('TR');for(var i=0;i<trs.length;i++){var cells=trs[i].cells;for(var j=0;j<cells.length;j++){var c=cells[j];var rowIndex=c.parentNode.rowIndex;var cellId=rowIndex+"-"+c.cellIndex;var rowSpan=c.rowSpan||1;var colSpan=c.colSpan||1
-var firstAvailCol;if(typeof(matrix[rowIndex])=="undefined"){matrix[rowIndex]=[];}for(var k=0;k<matrix[rowIndex].length+1;k++){if(typeof(matrix[rowIndex][k])=="undefined"){firstAvailCol=k;break;}}lookup[cellId]=firstAvailCol;for(var k=rowIndex;k<rowIndex+rowSpan;k++){if(typeof(matrix[k])=="undefined"){matrix[k]=[];}var matrixrow=matrix[k];for(var l=firstAvailCol;l<firstAvailCol+colSpan;l++){matrixrow[l]="x";}}}}return lookup;}function checkCellColSpan(table,rows,row){var arr=[],r=table.tHead.rows,c=r[row].cells;for(var i=0;i<c.length;i++){var cell=c[i];if(cell.colSpan>1){arr=arr.concat(checkCellColSpan(table,headerArr,row++));}else{if(table.tHead.length==1||(cell.rowSpan>1||!r[row+1])){arr.push(cell);}}}return arr;};function checkHeaderMetadata(cell){if(($.metadata)&&($(cell).metadata().sorter===false)){return true;};return false;}function checkHeaderOptions(table,i){if((table.config.headers[i])&&(table.config.headers[i].sorter===false)){return true;};return false;}function checkHeaderOptionsSortingLocked(table,i){if((table.config.headers[i])&&(table.config.headers[i].lockedOrder))return table.config.headers[i].lockedOrder;return false;}function applyWidget(table){var c=table.config.widgets;var l=c.length;for(var i=0;i<l;i++){getWidgetById(c[i]).format(table);}}function getWidgetById(name){var l=widgets.length;for(var i=0;i<l;i++){if(widgets[i].id.toLowerCase()==name.toLowerCase()){return widgets[i];}}};function formatSortingOrder(v){if(typeof(v)!="Number"){return(v.toLowerCase()=="desc")?1:0;}else{return(v==1)?1:0;}}function isValueInArray(v,a){var l=a.length;for(var i=0;i<l;i++){if(a[i][0]==v){return true;}}return false;}function setHeadersCss(table,$headers,list,css){$headers.removeClass(css[0]).removeClass(css[1]);var h=[];$headers.each(function(offset){if(!this.sortDisabled){h[this.column]=$(this);}});var l=list.length;for(var i=0;i<l;i++){h[list[i][0]].addClass(css[list[i][1]]);}}function fixColumnWidth(table,$headers){var c=table.config;if(c.widthFixed){var colgroup=$('<colgroup>');$("tr:first td",table.tBodies[0]).each(function(){colgroup.append($('<col>').css('width',$(this).width()));});$(table).prepend(colgroup);};}function updateHeaderSortCount(table,sortList){var c=table.config,l=sortList.length;for(var i=0;i<l;i++){var s=sortList[i],o=c.headerList[s[0]];o.count=s[1];o.count++;}}function multisort(table,sortList,cache){if(table.config.debug){var sortTime=new Date();}var dynamicExp="var sortWrapper = function(a,b) {",l=sortList.length;for(var i=0;i<l;i++){var c=sortList[i][0];var order=sortList[i][1];var s=(table.config.parsers[c].type=="text")?((order==0)?makeSortFunction("text","asc",c):makeSortFunction("text","desc",c)):((order==0)?makeSortFunction("numeric","asc",c):makeSortFunction("numeric","desc",c));var e="e"+i;dynamicExp+="var "+e+" = "+s;dynamicExp+="if("+e+") { return "+e+"; } ";dynamicExp+="else { ";}var orgOrderCol=cache.normalized[0].length-1;dynamicExp+="return a["+orgOrderCol+"]-b["+orgOrderCol+"];";for(var i=0;i<l;i++){dynamicExp+="}; ";}dynamicExp+="return 0; ";dynamicExp+="}; ";if(table.config.debug){benchmark("Evaling expression:"+dynamicExp,new Date());}eval(dynamicExp);cache.normalized.sort(sortWrapper);if(table.config.debug){benchmark("Sorting on "+sortList.toString()+" and dir "+order+" time:",sortTime);}return cache;};function makeSortFunction(type,direction,index){var a="a["+index+"]",b="b["+index+"]";if(type=='text'&&direction=='asc'){return"("+a+" == "+b+" ? 0 : ("+a+" === null ? 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