#2 Update to upstream release 1.3.0
Merged 2 years ago by jaruga. Opened 2 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

@@ -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

- 

@@ -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

- 

@@ -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

2 years ago

Pull-Request has been merged by jaruga

2 years ago