Name:		bowtie

Version:	1.2.3

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+

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

# 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

# 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

BuildRequires:	perl-interpreter

BuildRequires:	perl(Clone)

BuildRequires:	perl(Data::Dumper)

BuildRequires:	perl(Getopt::Long)

BuildRequires:	perl(Test::Deep)

BuildRequires:	python3

BuildRequires:	tbb-devel

BuildRequires:	zlib-devel

# 32-bit CPU architectures are not supported for bowtie version >= 1.1.0.

# https://github.com/BenLangmead/bowtie/commit/5f90d3fdad97a8181ddaa96c64faeef1f2b6edf9

ExcludeArch: i686 armv7hl

# 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

Provides: bundled(tiny-thread) = 1.1

%description

Bowtie, an ultrafast, memory-efficient short read aligner for short

DNA sequences (reads) from next-gen sequencers. Please cite: Langmead

B, et al. Ultrafast and memory-efficient alignment of short DNA

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

%prep

%setup -q

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

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

# 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}"

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.

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

# 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

# "Empty %%files file debugsourcefiles.list".

%make_build allall EXTRA_FLAGS="-g"

%install

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

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

cp -a reads %{buildroot}/%{_datadir}/bowtie/

cp -a indexes %{buildroot}/%{_datadir}/bowtie/

cp -a genomes %{buildroot}/%{_datadir}/bowtie/

cp -a scripts %{buildroot}/%{_datadir}/bowtie/

# Install bowtie-*-debug commands used by `bowtie --debug`.

for cmd in bowtie-*-debug; do

  cp -p "${cmd}" %{buildroot}/%{_bindir}/

done

%check

for cmd in bowtie bowtie-build bowtie-inspect; do

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

done

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

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

%dir %{_datadir}/bowtie

%{_bindir}/bowtie

%{_bindir}/bowtie-align-l

%{_bindir}/bowtie-align-l-debug

%{_bindir}/bowtie-align-s

%{_bindir}/bowtie-align-s-debug

%{_bindir}/bowtie-build

%{_bindir}/bowtie-build-l

%{_bindir}/bowtie-build-l-debug

%{_bindir}/bowtie-build-s

%{_bindir}/bowtie-build-s-debug

%{_bindir}/bowtie-inspect

%{_bindir}/bowtie-inspect-l

%{_bindir}/bowtie-inspect-l-debug

%{_bindir}/bowtie-inspect-s

%{_bindir}/bowtie-inspect-s-debug

%{_datadir}/bowtie/genomes

%{_datadir}/bowtie/indexes

%{_datadir}/bowtie/reads

%{_datadir}/bowtie/scripts

%changelog

* Fri Feb 28 2020 Jun Aruga <jaruga@redhat.com> - 1.2.3-1

- Update to upstream release 1.2.3

* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-13

- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild

* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-12

- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild

* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-11

- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-10

- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild

* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-9

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild

* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild

* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-7

- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild

* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-6

- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild

* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild

* Sat May 02 2015 Kalev Lember <kalevlember@gmail.com> - 1.0.1-4

- Rebuilt for GCC 5 C++11 ABI change

* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild

* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.0.1-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild

* Mon Jun 02 2014 Adam Huffman <bloch@verdurin.com> - 1.0.1-1

- Update to upstream release 1.0.1

* Wed Dec 04 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-2

- Correct licence information (thanks to Dave Love)

- Reorganise documentation (thanks to Dave Love)

- Fix compilation on ARM

* Wed Aug 07 2013 Adam Huffman <bloch@verdurin.com> - 1.0.0-1

- Update to stable upstream release 1.0.0

- Remove unnecessary script patch

* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-8

- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild

* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 0.12.7-7

- Perl 5.18 rebuild

* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-6

- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild

* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild

* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.12.7-4

- Rebuilt for c++ ABI breakage

* Mon Jan  9 2012 Adam Huffman <verdurin@fedoraproject.org> - 0.12.7-3

- add patch to fix compilation with GCC 4.7

* Mon Jun 27 2011 Adam Huffman <bloch@verdurin.com> - 0.12.7-2

- add missing doc/ 

- add patch to fix Perl script without shebang

* Mon Sep 13 2010 Adam Huffman <bloch@verdurin.com> - 0.12.7-1

- new upstream release 0.12.7

- changelog at http://bowtie-bio.sourceforge.net/index.shtml

* Tue Aug 31 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-3

- really fix compilation flags

* Wed Aug 25 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-2

- fix compilation flags

* Mon Aug  2 2010 Adam Huffman <bloch@verdurin.com> - 0.12.5-1

- initial version