Name: bowtie2

Version: 2.4.1

Release: 3%{?dist}

# Use the word "ultra fast" rather than "ultrafast".

# https://github.com/BenLangmead/bowtie2/issues/291

Summary: An ultra fast and memory-efficient read aligner

# * bowtie2: GPLv3+

# * TinyThread++: zlib, for files: tinythread.{h,cpp} fast_mutex.h

#   https://tinythreadpp.bitsnbites.eu/

#   https://gitorious.org/tinythread/tinythreadpp

License: GPLv3+ and zlib

URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Source0: https://github.com/BenLangmead/%{name}/archive/v%{version}.tar.gz

# Fix to build with given CXXFLAGS.

# https://github.com/BenLangmead/bowtie2/pull/296

Patch0: bowtie2-makefile-cxxflags.patch

BuildRequires: gcc-c++

BuildRequires: help2man

BuildRequires: libasan

BuildRequires: libubsan

BuildRequires: make

BuildRequires: perl-generators

BuildRequires: perl-interpreter

BuildRequires: perl(Clone)

BuildRequires: perl(File::Which)

BuildRequires: perl(FindBin)

BuildRequires: perl(Sys::Hostname)

BuildRequires: perl(Test::Deep)

BuildRequires: perl(lib)

BuildRequires: python3

%ifarch x86_64

BuildRequires: tbb-devel

%else

BuildRequires: simde-devel

%endif

BuildRequires: zlib-devel

# * 32-bit CPU architectures: not supported. See Makefile.

# * s390x: not ready to ship it. We take the conservative way.

#   as it is used for the research.

#   https://github.com/BenLangmead/bowtie2/issues/286

ExcludeArch: %{ix86} %{arm} s390x

# TinyThread++

Provides: bundled(tiny-thread) = 1.1

%description

Bowtie 2 is an ultra fast and memory-efficient tool for aligning sequencing

reads to long reference sequences. It is particularly good at aligning reads

of about 50 up to 100s or 1,000s of characters, and particularly good at

aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the

genome with an FM Index to keep its memory footprint small: for the human

genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports

gapped, local, and paired-end alignment modes.

%prep

%autosetup

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

rm -rf third_party

# Invalid double quote characters are used in the code.

# https://github.com/BenLangmead/bowtie2/issues/278

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

# Fix shebang to use the system interpreters.

sed -i '1s|/usr/bin/env perl|%{_bindir}/perl|' bowtie2

for file in bowtie2-{build,inspect}; do

  sed -i '1s|/usr/bin/env python3|%{__python3}|' "${file}"

done

%build

# Set build flags.

# https://src.fedoraproject.org/rpms/redhat-rpm-config/blob/master/f/buildflags.md

%set_build_flags

# Set flags considering the upstream testing cases for each architecture.

# https://github.com/BenLangmead/bowtie2/blob/master/.travis.yml

%ifnarch x86_64

export POPCNT_CAPABILITY=0

export NO_TBB=1

%endif

# Build with the target "all" rather than "allall"

# to skip the builds of debug and sanitized binaries

# saving the build time.

%make_build all

%install

%make_install PREFIX="%{_prefix}"

mkdir -p %{buildroot}%{_mandir}/man1

# Set version string explicitly to avoid showing the wrong command.

# https://github.com/BenLangmead/bowtie2/issues/294

for cmd in bowtie2 bowtie2-{build,inspect}; do

  help2man -N -s 1 -o "%{buildroot}%{_mandir}/man1/${cmd}.1" \

    --version-string="%{version}" \

    "%{buildroot}%{_bindir}/${cmd}"

done

%check

for cmd in bowtie2 bowtie2-{build,inspect}; do

  ./"${cmd}" --version | grep 'version %{version}'

done

# Skip tests for the debug and sanitized binaries not shipped.

sed -i '/my $binary_type/ s/"release", "debug", "sanitized"/"release"/' \

  scripts/test/simple_tests.pl

# See scripts/test/simple_tests.sh for the options.

ASAN_OPTIONS="halt_on_error=1" \

UBSAN_OPTIONS="halt_on_error=1" \

scripts/test/simple_tests.pl \

  --bowtie2=./bowtie2 \

  --bowtie2-build=./bowtie2-build \

  --compressed

%files

%doc AUTHORS MANUAL MANUAL.markdown NEWS TUTORIAL

%license LICENSE

%{_bindir}/bowtie2

%{_bindir}/bowtie2-align-l

%{_bindir}/bowtie2-align-s

%{_bindir}/bowtie2-build

%{_bindir}/bowtie2-build-l

%{_bindir}/bowtie2-build-s

%{_bindir}/bowtie2-inspect

%{_bindir}/bowtie2-inspect-l

%{_bindir}/bowtie2-inspect-s

%{_mandir}/man1/bowtie2.1*

%{_mandir}/man1/bowtie2-build.1*

%{_mandir}/man1/bowtie2-inspect.1*

%changelog

* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild

* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-2

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

* Sat Mar 28 2020 Jun Aruga <jaruga@redhat.com> - 2.4.1-1

- Initial package