[med-svn] r19528 - in trunk/packages/bowtie/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-07-05 19:05:34 +0000 (Sun, 05 Jul 2015)
New Revision: 19528

Added:
   trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch
Modified:
   trunk/packages/bowtie/trunk/debian/changelog
   trunk/packages/bowtie/trunk/debian/control
   trunk/packages/bowtie/trunk/debian/patches/series
   trunk/packages/bowtie/trunk/debian/rules
Log:
Enabling ppc64el on Makefile and debian/control


Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2015-07-05 18:03:41 UTC (rev 19527)
+++ trunk/packages/bowtie/trunk/debian/changelog	2015-07-05 19:05:34 UTC (rev 19528)
@@ -1,8 +1,13 @@
 bowtie (1.1.2-1) UNRELEASED; urgency=medium
 
   * New upstream version
+  * remove strange byte-compyled Python code bowtie-buildc (no idea how and
+    why it was created)
+  * Enabling ppc64el on Makefile and debian/control (Thanks for the patch to
+    Fernando Seiti Furusato <ferseiti at br.ibm.com>)
+    Closes: #788537
 
- -- Andreas Tille <tille at debian.org>  Sun, 05 Jul 2015 20:02:01 +0200
+ -- Andreas Tille <tille at debian.org>  Sun, 05 Jul 2015 20:03:54 +0200
 
 bowtie (1.1.1-2) unstable; urgency=high
 

Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control	2015-07-05 18:03:41 UTC (rev 19527)
+++ trunk/packages/bowtie/trunk/debian/control	2015-07-05 19:05:34 UTC (rev 19528)
@@ -16,7 +16,7 @@
 Homepage: http://bowtie-bio.sourceforge.net/
 
 Package: bowtie
-Architecture: amd64 kfreebsd-amd64
+Architecture: amd64 kfreebsd-amd64 ppc64el
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          python

Added: trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/ppc64el.patch	2015-07-05 19:05:34 UTC (rev 19528)
@@ -0,0 +1,48 @@
+Index: bowtie-1.1.1/Makefile
+===================================================================
+--- bowtie-1.1.1.orig/Makefile
++++ bowtie-1.1.1/Makefile
+@@ -4,7 +4,7 @@
+ 
+ SEQAN_DIR = /usr/include/seqan
+ SEQAN_INC = -I $(SEQAN_DIR)
+-INC = $(SEQAN_INC) -I third_party
++INC = $(SEQAN_INC)
+ CPP = g++
+ CXX = $(CPP)
+ CC = gcc
+@@ -42,7 +42,7 @@ ifneq (,$(findstring Darwin,$(shell unam
+     MACOS = 1
+ endif
+ 
+-ifneq (,$(findstring 13,$(shell uname -r)))
++ifneq (,$(findstring 12,$(shell uname -r)))
+ 	CPP = clang++
+ 	CC = clang
+ 	EXTRA_FLAGS += -stdlib=libstdc++
+@@ -75,11 +75,11 @@ else
+     PTHREAD_LIB = -lpthread
+ endif
+ 
+-POPCNT_CAPABILITY ?= 1
+-ifeq (1, $(POPCNT_CAPABILITY))
+-    EXTRA_FLAGS += -DPOPCNT_CAPABILITY
+-    INC += -I third_party
+-endif
++#POPCNT_CAPABILITY ?= 1
++#ifeq (1, $(POPCNT_CAPABILITY))
++#    EXTRA_FLAGS += -DPOPCNT_CAPABILITY
++#    INC += -I third_party
++#endif
+ 
+ PREFETCH_LOCALITY = 2
+ PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
+@@ -108,7 +108,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+ VERSION = $(shell cat VERSION)
+ 
+ BITS=32
+-ifeq (x86_64,$(shell uname -m))
++ifneq (,$(filter $(shell uname -m), ppc64le x86_64))
+ 	BITS=64
+ endif
+ # msys will always be 32 bit so look at the cpu arch instead.

Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	2015-07-05 18:03:41 UTC (rev 19527)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2015-07-05 19:05:34 UTC (rev 19528)
@@ -8,3 +8,4 @@
 seqan-popcount.patch
 # do_not_use_outdated_copy_of_cpuid_h.patch
 bowtie_ContextLss-1.1-1.4.patch
+ppc64el.patch

Modified: trunk/packages/bowtie/trunk/debian/rules
===================================================================
--- trunk/packages/bowtie/trunk/debian/rules	2015-07-05 18:03:41 UTC (rev 19527)
+++ trunk/packages/bowtie/trunk/debian/rules	2015-07-05 19:05:34 UTC (rev 19528)
@@ -23,6 +23,8 @@
              $(CURDIR)/bowtie-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-build.1
 	help2man --name="extracts information from a bowtie index" --no-info \
              $(CURDIR)/bowtie-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-inspect.1
+	# remove strange byte-compyled Python code bowtie-buildc (no idea how and why it was created)
+	find . -name bowtie-buildc -delete
 
 override_dh_compress:
 	dh_compress -X.ebwt