[med-svn] r13388 - in trunk/packages/bowtie/trunk/debian: . patches

[Ognyan Kulev]

Author: ogi
Date: 2013-04-24 08:00:53 +0000 (Wed, 24 Apr 2013)
New Revision: 13388

Added:
   trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
Modified:
   trunk/packages/bowtie/trunk/debian/README.source
   trunk/packages/bowtie/trunk/debian/changelog
   trunk/packages/bowtie/trunk/debian/control
   trunk/packages/bowtie/trunk/debian/patches/series
Log:
Depends on version 1.3 of SeqAn. Updated README.source. Removed machine bits detection.


Modified: trunk/packages/bowtie/trunk/debian/README.source
===================================================================
--- trunk/packages/bowtie/trunk/debian/README.source	2013-04-24 06:30:34 UTC (rev 13387)
+++ trunk/packages/bowtie/trunk/debian/README.source	2013-04-24 08:00:53 UTC (rev 13388)
@@ -1,12 +1,12 @@
 bowtie for Debian
 -----------------
 
-The bowtie package seems to rely on version 1.1 of the seqan library,
-while Debian otherwise already features version 1.2. It yet remains
-to be investigated, to what degree the two might possibly be
-compatible.
+The bowtie upstream source includes version 1.1 of SeqAn library and 
+uses it in compilation. This Debian package changes build process and 
+updates bowtie's source so that Debian's seqan package is used. If you 
+believe this leads to problems, please inform Debian maintainer or 
+Debian-Med team.
 
-We did not dare any respective experiments and hope for a clarification
-by upstream on this issue - we just should not introduce any hidden
-mistakes here.
-
+Bowtie build process have ability to select 32 or 64 bit version. This 
+is disabled and it is expected that users will use multiarch abilities 
+of Debian for choosing between running 32-bit or 64-bit version.

Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2013-04-24 06:30:34 UTC (rev 13387)
+++ trunk/packages/bowtie/trunk/debian/changelog	2013-04-24 08:00:53 UTC (rev 13388)
@@ -1,3 +1,11 @@
+bowtie (1.0.0-2) UNRELEASED; urgency=low
+
+  * Requires version 1.3 of SeqAn.
+  * Updated README.source about using Debian's SeqAn library.
+  * Removed machine_bits_detection.patch and added disable_bits_flag.patch.
+
+ -- Ognyan Kulev <ogi at debian.org>  Wed, 24 Apr 2013 10:49:47 +0300
+
 bowtie (1.0.0-1) unstable; urgency=low
 
   * New upstream version. (Closes: #705616)

Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control	2013-04-24 06:30:34 UTC (rev 13387)
+++ trunk/packages/bowtie/trunk/debian/control	2013-04-24 08:00:53 UTC (rev 13388)
@@ -7,7 +7,7 @@
  Yask Gupta <yask.gupta87 at gmail.com>,
  Andreas Tille <tille at debian.org>,
  Ognyan Kulev <ogi at debian.org>
-Build-Depends: debhelper (>= 9), help2man, seqan-dev
+Build-Depends: debhelper (>= 9), help2man, seqan-dev (>= 1.3)
 Standards-Version: 3.9.3
 Homepage: http://bowtie-bio.sourceforge.net/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk

Added: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch	2013-04-24 08:00:53 UTC (rev 13388)
@@ -0,0 +1,20 @@
+Description: Disable architecture bits detection.
+ In Debian, you can use multiarch facilities for choosing which version 
+ to run.
+Author: Ognyan Kulev <ogi at debian.org>
+Forwarded: not-needed 
+Last-Update: 2013-04-24 
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bowtie-1.0.0.orig/Makefile
++++ bowtie-1.0.0/Makefile
+@@ -121,6 +121,9 @@
+     BITS_FLAG = -m64
+ endif
+ 
++# Debian: Disable selection of 32/64-bits. Use multiarch instead.
++BITS_FLAG =
++
+ DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
+ RELEASE_FLAGS = -O3 $(BITS_FLAG)
+ NOASSERT_FLAGS = -DNDEBUG

Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	2013-04-24 06:30:34 UTC (rev 13387)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2013-04-24 08:00:53 UTC (rev 13388)
@@ -3,4 +3,4 @@
 seqan-fix-setBegin-call.patch
 seqan-rename-ChunkPool.patch
 seqan-rename-fill-to-resize.patch
-machine_bits_detection.patch
+disable_bits_flag.patch