Fix for review 3. (#2)

* Change the source to GitHub's one.
* Fix typo.
* Add man files.
* Build with %optflags.
* Convert 2 lines blank to 1 line blank too.

bowtie2-makefile-cxxflags.patch

@@ -0,0 +1,31 @@
+diff --git a/Makefile b/Makefile
+index 9b6a46e..df5a817 100644
+--- a/Makefile
++++ b/Makefile
+@@ -207,18 +207,18 @@ else ifeq (amd64,$(shell uname -m))
+ else ifeq (aarch64,$(shell uname -m))
+   BITS := 64
+   SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
+-  CPPFLAGS := -Ithird_party/simde
++  CXXFLAGS += -fopenmp-simd
++  CPPFLAGS += -Ithird_party/simde
+ else ifeq (s390x,$(shell uname -m))
+   BITS := 64
+   SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
+-  CPPFLAGS := -Ithird_party/simde
++  CXXFLAGS += -fopenmp-simd
++  CPPFLAGS += -Ithird_party/simde
+   SANITIZER_FLAGS :=
+ else ifeq (ppc64le,$(shell uname -m))
+   BITS := 64
+   SSE_FLAG :=
+-  CXXFLAGS := -fopenmp-simd
++  CXXFLAGS += -fopenmp-simd
+   CPPFLAGS += -Ithird_party/simde
+   SANITIZER_FLAGS :=
+ endif
+-- 
+2.25.4
+

bowtie2.spec

@@ -1,20 +1,22 @@
 Name: bowtie2
 Version: 2.4.1
 Release: 1%{?dist}
-Summary: An ultrafast and memory-efficient read aligner
+# 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://downloads.sourceforge.net/project/bowtie-bio/%{name}/%{version}/%{name}-%{version}-source.zip
-# git clone https://github.com/BenLangmead/bowtie2.git
-# cd bowtie2 && git checkout v2.4.1
-# tar czvf bowtie2-2.4.1-tests.tgz scripts/test/
-Source1: bowtie2-2.4.1-tests.tgz
+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
 Requires: python3
 BuildRequires: gcc-c++
+BuildRequires: help2man
 BuildRequires: libasan
 BuildRequires: libubsan
 BuildRequires: perl-generators
@@ -41,10 +43,9 @@ ExcludeArch: %{ix86} %{arm} s390x
 # TinyThread++
 Provides: bundled(tiny-thread) = 1.1
 
-
 %description
 
-Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing
+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
@@ -68,8 +69,10 @@ 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
@@ -82,18 +85,23 @@ export NO_TBB=1
 # 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
 
-tar xzvf %{SOURCE1}
-
 # 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
@@ -106,7 +114,6 @@ scripts/test/simple_tests.pl \
   --bowtie2-build=./bowtie2-build \
   --compressed
 
-
 %files
 %doc AUTHORS MANUAL MANUAL.markdown NEWS TUTORIAL
 %license LICENSE
@@ -119,7 +126,9 @@ scripts/test/simple_tests.pl \
 %{_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
 * Sat Mar 28 2020 Jun Aruga <jaruga@redhat.com> - 2.4.1-1