[med-svn] [bowtie2] 03/04: - d/changelog: new upstream version 2.2.0 - d/bowtie2.install, d/rules: new release introduces 2 new binaries: bowtie2-align-l and bowtie2-align-s instead of bowtie2-align - d/patches: refreshed

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository bowtie2.

commit e7790b28d593c713dba09796ba32d5f121c8ffb4
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Feb 20 13:30:20 2014 +0100

     - d/changelog: new upstream version 2.2.0
     - d/bowtie2.install, d/rules:
       new release introduces 2 new binaries: bowtie2-align-l and bowtie2-align-s
       instead of bowtie2-align
     - d/patches: refreshed
---
 debian/bowtie2.install                              |  4 ++--
 debian/changelog                                    |  6 ++++++
 debian/patches/fix_makefile_machine_detection.patch | 21 ++++++---------------
 debian/patches/hardening.patch                      |  2 +-
 debian/patches/series                               |  2 +-
 debian/rules                                        |  5 +++--
 6 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/debian/bowtie2.install b/debian/bowtie2.install
index f6a785f..dad02ea 100644
--- a/debian/bowtie2.install
+++ b/debian/bowtie2.install
@@ -1,5 +1,5 @@
 bowtie2		usr/bin
-bowtie2-align   usr/bin
+bowtie2-align-l usr/bin
+bowtie2-align-s usr/bin
 bowtie2-build   usr/bin
 bowtie2-inspect usr/bin
-
diff --git a/debian/changelog b/debian/changelog
index 5447250..e1642c8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bowtie2 (2.2.0-1) UNRELEASED; urgency=medium
+
+  * Imported Upstream version 2.2.0
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 20 Feb 2014 13:29:58 +0100
+
 bowtie2 (2.1.0-2) unstable; urgency=low
 
   * Closes: #713000 
diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
index 651f654..8397aed 100644
--- a/debian/patches/fix_makefile_machine_detection.patch
+++ b/debian/patches/fix_makefile_machine_detection.patch
@@ -1,17 +1,12 @@
-Subject: Attemp to adapt the build flags to built package on all supported 
- architectures.
-Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Date: 2013-02-28
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -117,27 +117,29 @@
+@@ -128,21 +128,29 @@
  SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
  VERSION = $(shell cat VERSION)
  
--# Convert BITS=?? to a -m flag
 -BITS=32
 -ifeq (x86_64,$(shell uname -m))
--BITS=64
+-	BITS=64
 -endif
 -# msys will always be 32 bit so look at the cpu arch instead.
 -ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
@@ -19,10 +14,8 @@ Date: 2013-02-28
 -		BITS=64
 -	endif
 -endif
--BITS_FLAG =
--
 -ifeq (32,$(BITS))
--	BITS_FLAG = -m32
+-  $(error bowtie2 compilation requires a 64-bit platform )
 -endif
 +ifeq (1,$(ENABLE_SSE))
 + ARCH := $(shell getconf LONG_BIT)
@@ -45,11 +38,9 @@ Date: 2013-02-28
 +       endif
 + endif
  
--ifeq (64,$(BITS))
--	BITS_FLAG = -m64
+-SSE_FLAG=-msse2 
 + SSE_FLAG=-msse2
- endif
--SSE_FLAG=-msse2
++endif
  
- DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 51f4b03..c1cd664 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,7 +2,7 @@ Subject: Patch injects hardening CPPFLAGS
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -204,7 +204,8 @@
+@@ -230,7 +230,8 @@
       $(FILE_FLAGS) \
       $(PREF_DEF) \
       $(MM_DEF) \
diff --git a/debian/patches/series b/debian/patches/series
index 8e9ce04..825a072 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-hardening.patch
 fix_makefile_machine_detection.patch
+hardening.patch
diff --git a/debian/rules b/debian/rules
index 5af98be..f65ad42 100755
--- a/debian/rules
+++ b/debian/rules
@@ -24,10 +24,11 @@ override_dh_auto_build:
 
 override_dh_installman:
 	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
-	debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align"
+	debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
 	debian/help2man-wrapper $(pkg)-build "building a colorspace index for $(pkg)"
 	debian/help2man-wrapper $(pkg)-inspect "extracts information from a $(pkg) index"
-	debian/help2man-wrapper $(pkg)-align "ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"
+	debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
+	debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
 
 override_dh_installchangelogs:
 	dh_installchangelogs NEWS

-- 
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