Name: bowtie2 Version: 2.4.1 Release: 6%{?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 * Wed Jul 20 2022 Fedora Release Engineering - 2.4.1-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jan 19 2022 Fedora Release Engineering - 2.4.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Wed Jul 21 2021 Fedora Release Engineering - 2.4.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Tue Jan 26 2021 Fedora Release Engineering - 2.4.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Mon Jul 27 2020 Fedora Release Engineering - 2.4.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Sat Mar 28 2020 Jun Aruga - 2.4.1-1 - Initial package