[med-svn] [bowtie] 01/01: Refresh patches

[Alex Mestiashvili]

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

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

commit cc286a991d50fea460262ff4861ae9cea86bdd91
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Oct 19 17:51:08 2017 +0200

    Refresh patches
---
 debian/patches/disable_bits_flag.patch   |  6 +++---
 debian/patches/enable_arm64.patch        |  6 +++---
 debian/patches/gcc-64bit.patch           |  6 +++---
 debian/patches/ppc64el.patch             | 10 +++++-----
 debian/patches/reproducible.patch        |  8 ++++----
 debian/patches/use-dpkg-buildflags.patch |  6 +++---
 debian/patches/use_debian_seqan.patch    |  6 +++---
 7 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/debian/patches/disable_bits_flag.patch b/debian/patches/disable_bits_flag.patch
index 89622b8..7811b75 100644
--- a/debian/patches/disable_bits_flag.patch
+++ b/debian/patches/disable_bits_flag.patch
@@ -5,9 +5,9 @@ Author: Ognyan Kulev <ogi at debian.org>
 Forwarded: not-needed 
 Last-Update: 2014-08-13 
 
---- a/Makefile
-+++ b/Makefile
-@@ -181,8 +181,8 @@ ifeq (32,$(BITS))
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -183,8 +183,8 @@
      $(error bowtie2 compilation requires a 64-bit platform )
  endif
  
diff --git a/debian/patches/enable_arm64.patch b/debian/patches/enable_arm64.patch
index 6518c09..1d2f3b7 100644
--- a/debian/patches/enable_arm64.patch
+++ b/debian/patches/enable_arm64.patch
@@ -3,9 +3,9 @@ Description: Enable arm64 architecture
 Bug-Debian: https://bugs.debian.org/800548
 Author: Edmund Grimley Evans <edmund.grimley.evans at gmail.com>
 Last-Update: Wed, 30 Sep 2015 19:09:04 +0100
---- a/Makefile
-+++ b/Makefile
-@@ -161,7 +161,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -163,7 +163,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/gcc-64bit.patch b/debian/patches/gcc-64bit.patch
index 9d2c0c3..770bb98 100644
--- a/debian/patches/gcc-64bit.patch
+++ b/debian/patches/gcc-64bit.patch
@@ -10,9 +10,9 @@ Description: Use gcc to determine if an arch is 64-bit
 Author: James Cowgill <jcowgill at debian.org>
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/Makefile
-+++ b/Makefile
-@@ -161,7 +161,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -163,7 +163,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/ppc64el.patch b/debian/patches/ppc64el.patch
index 46d14b8..38e6062 100644
--- a/debian/patches/ppc64el.patch
+++ b/debian/patches/ppc64el.patch
@@ -2,9 +2,9 @@ Description: enable for ppc64el
 Bug-Debian: https://bugs.debian.org/788537
 Author: Fernando Seiti Furusato <ferseiti at br.ibm.com>
 Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
---- a/Makefile
-+++ b/Makefile
-@@ -7,7 +7,7 @@ bindir = $(prefix)/bin
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -7,7 +7,7 @@
  
  SEQAN_DIR = /usr/include/seqan
  SEQAN_INC = -I $(SEQAN_DIR)
@@ -13,7 +13,7 @@ Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
  CPP = g++ -w
  CXX = $(CPP)
  CC = gcc
-@@ -102,11 +102,11 @@ else
+@@ -104,11 +104,11 @@
  	LIBS += $(PTHREAD_LIB)
  endif
  
@@ -30,7 +30,7 @@ Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
  
  PREFETCH_LOCALITY = 2
  PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
-@@ -161,7 +161,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+@@ -163,7 +163,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index 5812e80..e44bca9 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -1,8 +1,8 @@
 Description: make build reproducible
 Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/Makefile
-+++ b/Makefile
-@@ -243,9 +243,9 @@ allall: $(BIN_LIST) $(BIN_LIST_AUX)
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -245,9 +245,9 @@
  
  DEFS=-fno-strict-aliasing \
       -DBOWTIE_VERSION="\"`cat VERSION`\"" \
@@ -15,7 +15,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
       $(FILE_FLAGS) \
       $(PTHREAD_DEF) \
       $(PREF_DEF) \
-@@ -253,8 +253,8 @@ DEFS=-fno-strict-aliasing \
+@@ -255,8 +255,8 @@
       $(SHMEM_DEF)
  
  ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index f5e002d..ccb6e69 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -4,9 +4,9 @@ Author: Simon Ruderich <simon at ruderich.org>
 Last-Update: 2012-04-24
 Bug-Closed: http://bugs.debian.org/670230
 
---- a/Makefile
-+++ b/Makefile
-@@ -253,7 +253,7 @@ DEFS=-fno-strict-aliasing \
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -255,7 +255,7 @@
       $(MM_DEF) \
       $(SHMEM_DEF)
  
diff --git a/debian/patches/use_debian_seqan.patch b/debian/patches/use_debian_seqan.patch
index f0469b5..115124c 100644
--- a/debian/patches/use_debian_seqan.patch
+++ b/debian/patches/use_debian_seqan.patch
@@ -4,8 +4,8 @@ Date: 2011-01-30
 Last-Update: 2013-04-18
 Reviewed-by: Ognyan Kulev <ogi at debian.org>
 
---- a/Makefile
-+++ b/Makefile
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
 @@ -5,7 +5,7 @@
  prefix = /usr/local
  bindir = $(prefix)/bin
@@ -15,7 +15,7 @@ Reviewed-by: Ognyan Kulev <ogi at debian.org>
  SEQAN_INC = -I $(SEQAN_DIR)
  INC = $(SEQAN_INC) -I third_party
  CPP = g++ -w
-@@ -206,7 +206,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
+@@ -208,7 +208,6 @@
                 $(wildcard genomes/NC_008253.fna) \
                 $(wildcard reads/e_coli_1000.*) \
                 $(wildcard reads/e_coli_1000_*) \

-- 
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