debian/berkeley-express-doc.doc-base

+Document: express
+Title: doxygen documentation for eXpress
+Author: Adam Roberts, Lior Pachter
+Abstract: Streaming quantification for high-throughput sequencing
+ eXpress is a streaming tool for quantifying the abundances of a set of
+ target sequences from sampled subsequences. Example applications include
+ transcript-level RNA-Seq quantification, allele-specific/haplotype
+ expression analysis (from RNA-Seq), transcription factor binding
+ quantification in ChIP-Seq, and analysis of metagenomic data. It is
+ based on an online-EM algorithm that results in space (memory)
+ requirements proportional to the total size of the target sequences and
+ time requirements that are proportional to the number of sampled
+ fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
+ quantify much larger samples than other currently available tools
+ greatly reducing computing infrastructure requirements. eXpress can be
+ used to build lightweight high-throughput sequencing processing
+ pipelines when coupled with a streaming aligner (such as Bowtie), as
+ output can be piped directly into eXpress, effectively eliminating the
+ need to store read alignments in memory or on disk.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/berkeley-express/html/*
+Index: /usr/share/doc/berkeley-express/html/index.html

debian/berkeley-express-doc.install

+html		usr/share/doc/berkeley-express

debian/berkeley-express.install

 usr/bin/express usr/lib/debian-med/bin/
-html		usr/share/doc/berkeley-express
\ No newline at end of file

debian/changelog

@@ -17,6 +17,7 @@ berkeley-express (1.5.2+dfsg-1) UNRELEASED; urgency=medium
   * express-doc.pdf is not in upstream source any more
   * Exclude binaries and other unneeded files
   * provide html documentation
+  * avoid privace breach JS in html doc
 
  -- Steffen Moeller <moeller@debian.org>  Fri, 17 Nov 2017 23:39:43 +0100
 

debian/patches/privacy-breach.patch

+Description: avoid privace breach JS in html doc
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
+
+--- a/html/faq.html
++++ b/html/faq.html
+@@ -17,9 +17,6 @@
+   _gaq.push(['_trackPageview']);
+ 
+   (function() {
+-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+   })();
+ 
+ </script>
+@@ -90,15 +87,9 @@
+ 
+         <!-- Search form -->    
+ <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
+-<script src="http://www.google.com/jsapi" type="text/javascript"></script>
+ <script type="text/javascript"> 
+   google.load('search', '1', {language : 'en'});
+   google.setOnLoadCallback(function() {
+-    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
+-    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
+-    var options = new google.search.DrawOptions();
+-    options.enableSearchboxOnly("http://www.google.com/cse?cx=017113487431020499685:jdftct1emrw", null, true);
+-    customSearchControl.draw('cse-search-form', options);
+   }, true);
+ </script>
+ <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
+--- a/html/index.html
++++ b/html/index.html
+@@ -17,9 +17,6 @@
+   _gaq.push(['_trackPageview']);
+ 
+   (function() {
+-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+   })();
+ 
+ </script>
+@@ -95,15 +92,9 @@
+ 
+         <!-- Search form -->    
+ <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
+-<script src="http://www.google.com/jsapi" type="text/javascript"></script>
+ <script type="text/javascript"> 
+   google.load('search', '1', {language : 'en'});
+   google.setOnLoadCallback(function() {
+-    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
+-    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
+-    var options = new google.search.DrawOptions();
+-    options.enableSearchboxOnly("http://www.google.com/cse?cx=017113487431020499685:jdftct1emrw", null, true);
+-    customSearchControl.draw('cse-search-form', options);
+   }, true);
+ </script>
+ <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
+--- a/html/manual.html
++++ b/html/manual.html
+@@ -17,9 +17,6 @@
+   _gaq.push(['_trackPageview']);
+ 
+   (function() {
+-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+   })();
+ 
+ </script>
+@@ -89,7 +86,6 @@
+ 
+         <!-- Search form -->    
+ <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
+-<script src="http://www.google.com/jsapi" type="text/javascript"></script>
+ <script type="text/javascript"> 
+   google.load('search', '1', {language : 'en'});
+   google.setOnLoadCallback(function() {
+--- a/html/overview.html
++++ b/html/overview.html
+@@ -17,9 +17,6 @@
+   _gaq.push(['_trackPageview']);
+ 
+   (function() {
+-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+   })();
+ 
+ </script>
+@@ -91,15 +88,9 @@
+ 
+         <!-- Search form -->    
+ <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
+-<script src="http://www.google.com/jsapi" type="text/javascript"></script>
+ <script type="text/javascript"> 
+   google.load('search', '1', {language : 'en'});
+   google.setOnLoadCallback(function() {
+-    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
+-    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
+-    var options = new google.search.DrawOptions();
+-    options.enableSearchboxOnly("http://www.google.com/cse?cx=017113487431020499685:jdftct1emrw", null, true);
+-    customSearchControl.draw('cse-search-form', options);
+   }, true);
+ </script>
+ <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
+--- a/html/tutorial.html
++++ b/html/tutorial.html
+@@ -17,9 +17,6 @@
+   _gaq.push(['_trackPageview']);
+ 
+   (function() {
+-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+   })();
+ 
+ </script>
+@@ -89,15 +86,9 @@
+ 
+         <!-- Search form -->    
+ <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
+-<script src="http://www.google.com/jsapi" type="text/javascript"></script>
+ <script type="text/javascript"> 
+   google.load('search', '1', {language : 'en'});
+   google.setOnLoadCallback(function() {
+-    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
+-    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
+-    var options = new google.search.DrawOptions();
+-    options.enableSearchboxOnly("http://www.google.com/cse?cx=017113487431020499685:jdftct1emrw", null, true);
+-    customSearchControl.draw('cse-search-form', options);
+   }, true);
+ </script>
+ <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />

debian/patches/series

@@ -3,3 +3,4 @@ fix-bamtools-path
 drop-zlib
 gcc-6.patch
 correct-debug-flags.patch
+privacy-breach.patch