[med-svn] r9533 - trunk/packages/mummer/trunk/debian/patches

[Charles Plessy]

Author: plessy
Date: 2012-02-02 04:25:52 +0000 (Thu, 02 Feb 2012)
New Revision: 9533

Modified:
   trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
Log:
Refreshed (and corrected) the patch that links to PDFs on line.


Modified: trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff	2012-02-02 04:13:20 UTC (rev 9532)
+++ trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff	2012-02-02 04:25:52 UTC (rev 9533)
@@ -1,47 +1,47 @@
 Description: Some PDFs were removed and have to be downloaded from the upstream website instead.
 Origin: vendor : Debian
 Forwarded: not-needed
---- mummer-3.22~dfsg.orig/docs/web/index.html
-+++ mummer-3.22~dfsg/docs/web/index.html
+--- a/docs/web/index.html
++++ b/docs/web/index.html
 @@ -25,11 +25,11 @@
      detect similarity, then the PROmer program can generate alignments
      based upon the six-frame translations of both input sequences. The
      original MUMmer system, version 1.0, is described in our <a
 -    href=MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
-+    href=http://mummer.sourceforge.net/MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
++    href="http://mummer.sourceforge.net/MUMmer.pdf">1999 <em>Nucleic Acids Research</em> paper</a>.
      Version 2.1 appeared a few years later and is described in our <a
 -    href=MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
-+    href=http://mummer.sourceforge.net/MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
++    href="http://mummer.sourceforge.net/MUMmer2.pdf">2002 <em>Nucleic Acids Research</em> paper</a>,
      while MUMmer 3.0 was recently described in our <a
--    href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
-+    href=http://mummer.sourceforge.net/MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
+-    href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. We have also developed a GPU accelerated version of MUMmer called <a href="http://mummergpu.sf.net">MUMmerGPU</a>.</p>
++    href="http://mummer.sourceforge.net/MUMmer3.pdf">2004 <em>Genome Biology</em> paper</a>. We have also developed a GPU accelerated version of MUMmer called <a href="http://mummergpu.sf.net">MUMmerGPU</a>.</p>
+ 
+ <p> For more
      information regarding the MUMmer package, please refer to the:</p>
- 
-     <big><b><a
-@@ -172,7 +172,7 @@
+@@ -174,7 +174,7 @@
    <h3><em><font color="#CC0000"> Applications </font></em></h3>
    <p>MUMmer 1 was used to detect numerous large-scale inversions in
      bacterial genomes, leading to a new model of chromosome
 -    inversions, reported in this <a href=XFiles.pdf>2000 <em>Genome
-+    inversions, reported in this <a href=http://mummer.sourceforge.net/XFiles.pdf>2000 <em>Genome
++    inversions, reported in this <a href="http://mummer.sourceforge.net/XFiles.pdf">2000 <em>Genome
      Biology</em> paper</a>. It was also used to discover evidence for
      a recent whole-genome duplication in <em>Arabidopsis
      thaliana</em>, reported in "Analysis of the genome sequence of the
-@@ -227,14 +227,14 @@
+@@ -229,14 +229,14 @@
    <p><a href="manual">MUMmer 3 user manual</a></p>
    <p><a href="examples">MUMmer 3 examples</a></p>
    <p>Open source MUMmer 3.0 is described in "<a
 -        href=MUMmer3.pdf>Versatile and open software for comparing large genomes</a>." 
-+        href=http://mummer.sourceforge.net/MUMmer3.pdf>Versatile and open software for comparing large genomes</a>." 
++        href="http://mummer.sourceforge.net/MUMmer3.pdf">Versatile and open software for comparing large genomes</a>." 
      S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, 
      and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
 -  <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=MUMmer2.pdf>Fast 
-+  <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=http://mummer.sourceforge.net/MUMmer2.pdf>Fast 
++  <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href="http://mummer.sourceforge.net/MUMmer2.pdf">Fast 
      Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher, 
      A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em> 
      (2002), Vol. 30, No. 11 2478-2483.</p>
 -  <p>MUMmer 1.0 is described in "<a href=MUMmer.pdf>Alignment of Whole Genomes</a>." 
-+  <p>MUMmer 1.0 is described in "<a href=http://mummer.sourceforge.net/MUMmer.pdf>Alignment of Whole Genomes</a>." 
++  <p>MUMmer 1.0 is described in "<a href="http://mummer.sourceforge.net/MUMmer.pdf">Alignment of Whole Genomes</a>." 
      A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. 
      Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
    <p>Space efficent suffix trees are described in "<a