[med-svn] r18227 - in trunk/packages/bowtie/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-10-06 16:54:05 +0000 (Mon, 06 Oct 2014)
New Revision: 18227

Added:
   trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch
Modified:
   trunk/packages/bowtie/trunk/debian/changelog
   trunk/packages/bowtie/trunk/debian/control
   trunk/packages/bowtie/trunk/debian/patches/series
Log:
Further patch to adapt to SeqAn 1.4 (thanks to Gert Wollny); Python dependency


Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2014-10-06 12:54:03 UTC (rev 18226)
+++ trunk/packages/bowtie/trunk/debian/changelog	2014-10-06 16:54:05 UTC (rev 18227)
@@ -1,7 +1,9 @@
-bowtie (1.1.1-1) UNRELEASED; urgency=medium
+bowtie (1.1.1-1) unstable; urgency=medium
 
   * New upstream release
   * cme fix dpkg-control
+  * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
+  * Add Depends: python (also Build-Depends since it is used in tests)
 
  -- Andreas Tille <tille at debian.org>  Thu, 02 Oct 2014 14:32:50 +0200
 

Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control	2014-10-06 12:54:03 UTC (rev 18226)
+++ trunk/packages/bowtie/trunk/debian/control	2014-10-06 16:54:05 UTC (rev 18227)
@@ -8,7 +8,8 @@
 Priority: optional
 Build-Depends: debhelper (>= 9),
                help2man,
-               seqan-dev (>= 1.4)
+               seqan-dev (>= 1.4),
+               python
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/
@@ -17,7 +18,8 @@
 Package: bowtie
 Architecture: amd64 kfreebsd-amd64
 Depends: ${shlibs:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         python
 Suggests: bowtie-examples
 Description: Ultrafast memory-efficient short read aligner
  This package addresses the problem to interpret the results from the

Added: trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch	2014-10-06 16:54:05 UTC (rev 18227)
@@ -0,0 +1,18 @@
+Description: Change class name of _Context_LSS
+ New version 1.4 of SeQan uses a different name of the class. 
+Forwarded: no
+Author: Gert Wollny <gw.fossdev at gmail.com>
+Last-Update: 2014-100-06
+
+--- a/diff_sample.h
++++ b/diff_sample.h
+@@ -853,7 +856,7 @@
+ 	{
+ 		Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());
+ 		VMSG_NL("  Invoking Larsson-Sadakane on ranks");
+-		_Context_LSS<TIndexOff> c;
++		ContextLss_<TIndexOff> c;
+ 		c.suffixsort(
+ 			(TIndexOff*)begin(_isaPrime, Standard()),
+ 			(TIndexOff*)begin(sPrime, Standard()),
+

Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	2014-10-06 12:54:03 UTC (rev 18226)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2014-10-06 16:54:05 UTC (rev 18227)
@@ -7,3 +7,4 @@
 no_hash_style_both_for_mips.patch
 seqan-popcount.patch
 # do_not_use_outdated_copy_of_cpuid_h.patch
+bowtie_ContextLss-1.1-1.4.patch