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#2 Update to upstream release 1.3.0
Merged 3 years ago by jaruga. Opened 3 years ago by jaruga.
rpms/ jaruga/bowtie wip/update-to-1.3.0  into  master

file modified
+2 
@@ -3,3 +3,5 @@ 
 

  /bowtie-1.0.1-src.zip
 

  /bowtie-1.2.3-tests.tgz
 

  /bowtie-src-x86_64.zip
 

+ /bowtie-1.3.0-src.zip
 

+ /bowtie-1.3.0-tests.tgz

file removed
-29 
@@ -1,29 +0,0 @@ 
 

- diff --git a/alphabet.cpp b/alphabet.cpp
 

- index fe94493..6b7ff30 100644
 

- --- a/alphabet.cpp
 

- +++ b/alphabet.cpp
 

- @@ -273,7 +273,7 @@ int dnacomp[5] = {
 

-  

-  const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
 

-  

- -char mask2iupac[16] = {
 

- +signed char mask2iupac[16] = {
 

-  	-1,
 

-  	'A', // 0001
 

-  	'C', // 0010
 

- diff --git a/alphabet.h b/alphabet.h
 

- index fc03779..35a5699 100644
 

- --- a/alphabet.h
 

- +++ b/alphabet.h
 

- @@ -227,7 +227,7 @@ extern uint8_t nuccol2nuc[5][5];
 

-  extern uint8_t asc2dnamask[];
 

-  

-  /// Convert a 4-bit mask into an IUPAC code
 

- -extern char mask2iupac[16];
 

- +extern signed char mask2iupac[16];
 

-  

-  /**
 

-   * Return true iff c is an unambiguous Dna character.
 

- -- 

- 2.24.1
 

-

file removed
-46 
@@ -1,46 +0,0 @@ 
 

- diff --git a/Makefile b/Makefile
 

- index bbce0a2..9cac1fe 100644
 

- --- a/Makefile
 

- +++ b/Makefile
 

- @@ -8,10 +8,10 @@ bindir = $(prefix)/bin
 

-  SEQAN_DIR = ./SeqAn-1.1
 

-  # treat SeqAn as a sysdir to suppress warnings
 

-  SEQAN_INC = -isystem $(SEQAN_DIR)
 

- -INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
 

- -CPP = g++
 

- -CXX = $(CPP)
 

- -CC = gcc
 

- +INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC)
 

- +CPP ?= g++
 

- +CXX ?= $(CPP)
 

- +CC ?= gcc
 

-  LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
 

-  HEADERS = $(wildcard *.h)
 

-  BOWTIE_MM = 1
 

- @@ -162,6 +162,12 @@ VERSION = $(shell cat VERSION)
 

-  BITS=32
 

-  ifeq (x86_64,$(shell uname -m))
 

-  	BITS=64
 

- +else ifeq (aarch64,$(shell uname -m))
 

- +	BITS=64
 

- +else ifeq (s390x,$(shell uname -m))
 

- +	BITS=64
 

- +else ifeq (ppc64le,$(shell uname -m))
 

- +	BITS=64
 

-  endif
 

-  # msys will always be 32 bit so look at the cpu arch instead.
 

-  ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
 

- @@ -180,8 +186,8 @@ ifeq (32,$(BITS))
 

-      $(error bowtie2 compilation requires a 64-bit platform )
 

-  endif
 

-  

- -DEBUG_FLAGS = -O0 -g3 -m64
 

- -RELEASE_FLAGS = -O3 -m64
 

- +DEBUG_FLAGS = -O0 -g3
 

- +RELEASE_FLAGS = -O3
 

-  NOASSERT_FLAGS = -DNDEBUG
 

-  FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 

-  

- -- 

- 2.24.1
 

-

file added
+36 
@@ -0,0 +1,36 @@ 
 

+ From ea04fb256aa01ca1252613c5d5de3c9e2d6327ee Mon Sep 17 00:00:00 2001
 

+ From: Rone Charles <rone_charles@fastmail.com>
 

+ Date: Mon, 27 Jul 2020 19:19:34 -0400
 

+ Subject: [PATCH] Potential fix for cpu_backoff related errors on ppc
 

+ 

+ ---
 

+  bt2_locks.h | 8 ++++++--
 

+  1 file changed, 6 insertions(+), 2 deletions(-)
 

+ 

+ diff --git a/bt2_locks.h b/bt2_locks.h
 

+ index b956ea4..cddbd8b 100644
 

+ --- a/bt2_locks.h
 

+ +++ b/bt2_locks.h
 

+ @@ -12,13 +12,17 @@
 

+  class cpu_backoff {
 

+  public:
 

+  	cpu_backoff(): count(1) {}
 

+ -	void pause() {
 

+ +	inline void pause() {
 

+  		if (count <= LOOPS_BEFORE_YIELD) {
 

+  			for (int32_t i = 0; i < count; i++) {
 

+  #ifdef __aarch64__
 

+  				__asm__ __volatile__("yield" ::: "memory");
 

+ -#else
 

+ +#elif __ppc__
 

+ +				__asm__ __volatile__("or 27,27,27" ::: "memory");
 

+ +#elif __x86_64__
 

+  				__asm__ __volatile__("pause;");
 

+ +#else
 

+ +				// do nothing
 

+  #endif
 

+  			}
 

+  			count *= 2;
 

+ -- 

+ 2.26.2
 

+

file modified
+18 -45 
@@ -1,31 +1,23 @@ 
 

  Name:		bowtie
 

- Version:	1.2.3
 

- Release:	3%{?dist}
 

+ Version:	1.3.0
 

+ Release:	1%{?dist}
 

  Summary:	An ultrafast, memory-efficient short read aligner
 

  

  # bowite: Artistic 2.0
 

  # tinythread.{h,cpp}: zlib
 

- # SeqAn: GPLv3 and LGPLv3+
 

- # SeqAn license info is not enough?
 

- # https://github.com/BenLangmead/bowtie/issues/106
 

- License:	Artistic 2.0 and zlib and GPLv3 and LGPLv3+
 

+ License:	Artistic 2.0 and zlib
 

  URL:		http://bowtie-bio.sourceforge.net/index.shtml
 

- # bowtie v1.2.3 archive file name is wrong.
 

- # https://github.com/BenLangmead/bowtie/issues/101
 

- Source0:	http://downloads.sourceforge.net/%{name}-bio/%{name}-src-x86_64.zip
 

+ Source0:	http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip
 

  # git clone https://github.com/BenLangmead/bowtie.git
 

  # cd bowtie
 

- # git checkout v1.2.3
 

- # tar czvf bowtie-1.2.3-tests.tgz scripts/test/
 

- Source1:	bowtie-1.2.3-tests.tgz
 

- # Enable multiple CPU architecture builds.
 

- # https://github.com/BenLangmead/bowtie/pull/102
 

- Patch0:		bowtie-enable-multi-arch.patch
 

+ # git checkout v1.3.0
 

+ # tar czvf bowtie-1.3.0-tests.tgz scripts/test/
 

+ Source1:	bowtie-%{version}-tests.tgz
 

+ # Fix bt2_locks.h: Error: Unrecognized opcode: `pause' on ppc64le/s390x.
 

+ # https://github.com/BenLangmead/bowtie/issues/114
 

+ Patch0:		bowtie-fix-ppc64le-s390x-asm-pause-error.patch
 

  # Remove perl-Sys-Info module depenency, as it does not exist on Fedora.
 

  Patch1:		bowtie-test-remove-perl-Sys-Info-dep.patch
 

- # Fix error narrowing conversion for non x86_64 architectures.
 

- # https://github.com/BenLangmead/bowtie/pull/95
 

- Patch2:		bowtie-alphabet-error-narrowing.patch
 

  Requires:	python3
 

  BuildRequires:	gcc-c++
 

  BuildRequires:	hostname
 
@@ -45,15 +37,6 @@ 
 

  

  # Bundled libraries
 

  # https://fedoraproject.org/wiki/Bundled_Libraries?rd=Packaging:Bundled_Libraries#Requirement_if_you_bundle
 

- # SeqAn
 

- # http://www.seqan.de/
 

- # TODO: Use system seqan instead of bundled one.
 

- # https://src.fedoraproject.org/rpms/seqan
 

- # Update to seqan 1.4.2
 

- # https://github.com/BenLangmead/bowtie/pull/105
 

- # Note SeqAn will be removed at tne next release of version 1.2.3.
 

- # https://github.com/BenLangmead/bowtie/issues/106#issuecomment-593426727
 

- Provides: bundled(seqan) = 1.1
 

  # TinyThread++
 

  # https://tinythreadpp.bitsnbites.eu/
 

  # https://gitorious.org/tinythread/tinythreadpp
 
@@ -68,24 +51,18 @@ 
 

  sequences to the human genome. Genome Biol 10:R25.
 

  

  %prep
 

- %setup -q
 

+ %setup -q -n %{name}-%{version}-src
 

  

- %patch0 -p1 -b .bowtie-enable-multi-arch.patch
 

- %patch2 -p1 -b .bowtie-alphabet-error-narrowing.patch
 

+ %patch0 -p1
 

  

  # Remove the directory to avoid building bowtie with bundled libraries.
 

  rm -rf third_party/
 

  

  # Fix shebang to use system python3.
 

  for file in $(find . -name "*.py") bowtie bowtie-*; do
 

-   sed -i '1s|/usr/bin/env python|%{__python3}|' "${file}"
 

+   sed -E -i '1s|/usr/bin/env python[3]?|%{__python3}|' "${file}"
 

  done
 

  

- # Invalid double quote characters are used in the code.
 

- # https://github.com/BenLangmead/bowtie/issues/104
 

- sed -i 's/“/"/g' processor_support.h
 

- sed -i 's/”/"/g' processor_support.h
 

- 

  

  %build
 

  # Set flags considering bowtie2's testing cases for each architecture.
 
@@ -93,7 +70,6 @@ 
 

  # https://github.com/BenLangmead/bowtie/pull/102
 

  %ifnarch x86_64
 

  export POPCNT_CAPABILITY=0
 

- export NO_TBB=1
 

  %endif
 

  

  # Set debug flag "-g" to prevent the error
 
@@ -102,7 +78,7 @@ 
 

  

  

  %install
 

- %make_install prefix="%{_usr}" DESTDIR="%{buildroot}"
 

+ %make_install prefix="%{_prefix}"
 

  

  mkdir -p %{buildroot}/%{_datadir}/bowtie
 

  cp -a reads %{buildroot}/%{_datadir}/bowtie/
 
@@ -123,18 +99,12 @@ 
 

  tar xzvf %{SOURCE1}
 

  cat %{PATCH1} | patch -p1
 

  

- %ifarch s390x
 

- # The tests works with the number of thread: 1 on s390x.
 

- # https://github.com/BenLangmead/bowtie/pull/105
 

- sed -i 's/--threads $nthreads/--threads 1/' scripts/test/simple_tests.pl
 

- %endif
 

- 

  # See Makefile simple-test target.
 

  scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
 

  

  

  %files
 

- %license LICENSE SeqAn-1.1/{GPL,LGPL}.txt
 

+ %license LICENSE
 

  %doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css}
 

  %dir %{_datadir}/bowtie
 

  %{_bindir}/bowtie
 
@@ -159,6 +129,9 @@ 
 

  

  

  %changelog
 

+ * Tue Jul 28 2020 Jun Aruga <jaruga@redhat.com> - 1.3.0-1
 

+ - Update to upstream release 1.3.0
 

+ 

  * Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.3-3
 

  - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild

file modified
+2 -2 
@@ -1,2 +1,2 @@ 
 

- SHA512 (bowtie-1.2.3-tests.tgz) = 810120e7acc91cbc06dceba2387b921ada3644f63c3ffce4237fbb7edf317f8dba11d250e49dfb702ea3245dba27091f98bf3dec0b4c22b25e5b67fd2e78f5d3
 

- SHA512 (bowtie-src-x86_64.zip) = 3d902b8a060f1a6af41602c5169bea0b43a5d0f2f0c72286602dcd5f84c42f261d93acc05baa45a34a57fe9f2d223e3917b1aa29c7cb93d93f93b86a3f365174
 

+ SHA512 (bowtie-1.3.0-src.zip) = 27c33221a395de6dbf086c63befd007ac6033ab0fca6ce6b79b6c13de6bd02d5585c0c38c442e50dca5cdf95cfca136310ace334bbf24ac90e8e7aece93001a7
 

+ SHA512 (bowtie-1.3.0-tests.tgz) = 9e25cbba3da9085b8427a0e2df77c21864c7bfbf51aced784362873c801bee92a95456bbd5b1ea02bf4a4443edba748e830fe9b8fea95f0c61e37f6297f4383c

This PR is to upgrade bowtie to the latest version 1.3.0.
The PR is to show the actual log. I will merge the PR immediately in the current situation.

rebased onto 1862384
3 years ago

Pull-Request has been merged by jaruga
3 years ago
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Changes Summary 6
+2 -0
file changed
.gitignore
-29
file removed
bowtie-alphabet-error-narrowing.patch
-46
file removed
bowtie-enable-multi-arch.patch
+36
file added
bowtie-fix-ppc64le-s390x-asm-pause-error.patch
+18 -45
file changed
bowtie.spec
+2 -2
file changed
sources
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