PR#1: Update to upstream release 1.2.3 - rpms/bowtie

rpms / bowtie

#1 Update to upstream release 1.2.3

Merged 4 years ago by jaruga. Opened 4 years ago by jaruga.

rpms/ jaruga/bowtie feature/update-to-v1.2.3 into master

Update to upstream release 1.2.3

Jun Aruga • 4 years ago

8f1cc3a

.gitignore

file modified

+2 -1

		`@@ -1,4 +1,5 @@`
		`/bowtie-0.12.7-src.zip`
		`/bowtie-1.0.0-src.zip`
		`- /bowtie-arm-gcc.patch`
		`/bowtie-1.0.1-src.zip`
		`+ /bowtie-1.2.3-tests.tgz`
		`+ /bowtie-src-x86_64.zip`

bowtie-alphabet-error-narrowing.patch

file added

+29

		`@@ -0,0 +1,29 @@`
		`+ 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`
		`+`

bowtie-enable-multi-arch.patch

file added

+46

		`@@ -0,0 +1,46 @@`
		`+ 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`
		`+`

bowtie-gcc47.patch

file removed

-39

		`@@ -1,39 +0,0 @@`
		`- --- bowtie-0.12.7/alphabet.h 2009-11-24 20:53:52.000000000 +0000`
		`- +++ bowtie-0.12.7.new/alphabet.h 2012-01-09 10:53:09.902974406 +0000`
		`- @@ -38,6 +38,18 @@`
		`- return s_rc;`
		`- }`
		`-`
		`- +/// Reverse a string in-place`
		`- +template <typename TStr>`
		`- +static inline void reverseInPlace(TStr& s) {`
		`- + typedef typename Value<TStr>::Type TVal;`
		`- + size_t len = length(s);`
		`- + for(size_t i = 0; i < (len>>1); i++) {`
		`- + TVal tmp = s[i];`
		`- + s[i] = s[len-i-1];`
		`- + s[len-i-1] = tmp;`
		`- + }`
		`- +}`
		`- +`
		`- /**`
		`- * Reverse-complement s in-place. Ns go to Ns.`
		`- */`
		`- @@ -69,17 +81,6 @@`
		`- }`
		`- }`
		`-`
		`- -/// Reverse a string in-place`
		`- -template <typename TStr>`
		`- -static inline void reverseInPlace(TStr& s) {`
		`- - typedef typename Value<TStr>::Type TVal;`
		`- - size_t len = length(s);`
		`- - for(size_t i = 0; i < (len>>1); i++) {`
		`- - TVal tmp = s[i];`
		`- - s[i] = s[len-i-1];`
		`- - s[len-i-1] = tmp;`
		`- - }`
		`- -}`
		`-`
		`- /**`
		`- * Return the reverse-complement of s.`

bowtie-script-shebang.patch

file removed

-8

		`@@ -1,8 +0,0 @@`
		`- diff -ur bowtie-0.12.7/scripts/gen_dnamasks2colormask.pl bowtie-0.12.7.new/scripts/gen_dnamasks2colormask.pl`
		`- --- bowtie-0.12.7/scripts/gen_dnamasks2colormask.pl 2010-06-06 15:36:31.000000000 +0100`
		`- +++ bowtie-0.12.7.new/scripts/gen_dnamasks2colormask.pl 2011-06-27 22:56:01.673782736 +0100`
		`- @@ -1,3 +1,4 @@`
		`- +#!/usr/bin/perl -w`
		`- print "uint8_t dnamasks2colormask[16][16] = {\n";`
		`- print "\t /* 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 */\n";`
		`- my %color = (`

bowtie-test-remove-perl-Sys-Info-dep.patch

file added

+28

		`@@ -0,0 +1,28 @@`
		`+ diff --git a/scripts/test/simple_tests.pl b/scripts/test/simple_tests.pl`
		`+ index d8b452f..ad932f5 100755`
		`+ --- a/scripts/test/simple_tests.pl`
		`+ +++ b/scripts/test/simple_tests.pl`
		`+ @@ -14,8 +14,6 @@ use Data::Dumper;`
		`+ use DNA;`
		`+ use Clone qw(clone);`
		`+ use Test::Deep;`
		`+ -use Sys::Info;`
		`+ -use Sys::Info::Constants qw( :device_cpu );`
		`+`
		`+ my $bowtie = "";`
		`+ my $bowtie_build = "";`
		`+ @@ -1130,9 +1128,8 @@ sub runbowtie($$$$$$$$$$$$$$$$$$$$$$$) {`
		`+ while(<FA>) { print $_; }`
		`+ close(FA);`
		`+ if($do_build) {`
		`+ - my $info = Sys::Info->new;`
		`+ - my $cpu = $info->device('CPU');`
		`+ - my $nthreads = int(rand($cpu->count \|\| 1)) + 1;`
		`+ + my $cpu_count = 2;`
		`+ + my $nthreads = int(rand($cpu_count \|\| 1)) + 1;`
		`+ my $build_args = "";`
		`+ $build_args .= " -C " if $color;`
		`+ my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";`
		`+ --`
		`+ 2.21.0`
		`+`

bowtie.spec

file modified

+120 -25

		`@@ -1,17 +1,61 @@`
		`Name: bowtie`
		`- Version: 1.0.1`
		`- Release: 14%{?dist}`
		`+ Version: 1.2.3`
		`+ Release: 1%{?dist}`
		`Summary: An ultrafast, memory-efficient short read aligner`

		`- # The tinythread component is zlib-like, SeqAn is LGPL`
		`- License: Artistic 2.0 and zlib and LGPLV3+`
		`+ # 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`
		`- Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip`
		`- Patch0: %{name}-arm-gcc.patch`
		`- #Patch0: %{name}-script-shebang.patch`
		`- #Patch1: %{name}-gcc47.patch`
		`- BuildRequires: gcc-c++`
		`- BuildRequires: perl-generators`
		`+ # 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`
		`@@ -24,47 +68,98 @@`
		`%prep`
		`%setup -q`

		`- #Fix compilation on ARM by removing hard-coded Makefile GCC directives`
		`- %patch0 -p1 -b .%{name}-arm-gcc.patch`
		`+ %patch0 -p1 -b .bowtie-enable-multi-arch.patch`
		`+ %patch2 -p1 -b .bowtie-alphabet-error-narrowing.patch`

		`- #%patch0 -p1`
		`- #Fix compilation with GCC 4.7`
		`- #%patch1 -p1 -b .%{name}-gcc47.patch`
		`+ # Remove the directory to avoid building bowtie with bundled libraries.`
		`+ rm -rf third_party/`

		`- %build`
		`- make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}"`
		`+ # 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`

		`- %install`
		`- rm -rf %{buildroot}`

		`- mkdir -p %{buildroot}/%{_bindir}`
		`- mkdir -p %{buildroot}/%{_datadir}/bowtie`
		`+ %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 -m 0755 bowtie %{buildroot}/%{_bindir}`
		`- install -m 0755 bowtie-build %{buildroot}/%{_bindir}`
		`- install -m 0755 bowtie-inspect %{buildroot}/%{_bindir}`

		`+ %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`
		`- %doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css} SeqAn-1.1/*GPL.txt`
		`+ %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`
		`+`
		`* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.1-14`
		`- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild`

sources

file modified

+2 -2

		`@@ -1,2 +1,2 @@`
		`- 8484fba71f78d94ee9e16a9b5c8c8d26 bowtie-1.0.1-src.zip`
		`- 83ecb7f17abdd274751ecc1dfc48cd4e bowtie-arm-gcc.patch`
		`+ SHA512 (bowtie-1.2.3-tests.tgz) = 810120e7acc91cbc06dceba2387b921ada3644f63c3ffce4237fbb7edf317f8dba11d250e49dfb702ea3245dba27091f98bf3dec0b4c22b25e5b67fd2e78f5d3`
		`+ SHA512 (bowtie-src-x86_64.zip) = 3d902b8a060f1a6af41602c5169bea0b43a5d0f2f0c72286602dcd5f84c42f261d93acc05baa45a34a57fe9f2d223e3917b1aa29c7cb93d93f93b86a3f365174`

jaruga commented 4 years ago

This PR is to update bowtie to the latest version 1.2.3.

This PR is working in progress.

Because I am trying to use rpms/seaqn version 1.4.2 (= The latest version of 1.X) in bowtie.spec, sending the PR to the bowite upstream.
https://github.com/BenLangmead/bowtie/pull/105

seqan
http://packages.seqan.de/
https://github.com/seqan/seqan

Because on Fedora, using dependency RPM is encouraged rather than using bundled library.
https://fedoraproject.org/wiki/Bundled_Libraries?rd=Packaging:Bundled_Libraries

Another note is right now bowtie-arm-gcc.patch is registered like a source.
This is wrong state.

$ cat sources 
8484fba71f78d94ee9e16a9b5c8c8d26  bowtie-1.0.1-src.zip
83ecb7f17abdd274751ecc1dfc48cd4e  bowtie-arm-gcc.patch

We can fix this by running fepkg import for the updated bowite.spec.

$ fepkg import bowtie-1.2.3-1.fc33.src.rpm

Dependency check: Is other packages using bowtie as BuildRequire or Require?: No. (OK)
License check: working in progress.
Maybe we can use seqan-devel (version 1.4.2) as the build dependency.
See my upstream work to use seqan 1.4.2.
https://github.com/BenLangmead/bowtie/pull/105
rpmlint check:-
Install check: ok
Running bowtie command on mock environment: working in progress.
Scratch build: ok
https://koji.fedoraproject.org/koji/taskinfo?taskID=41998858

rpmlint

You can check the rpmlint like this.

$ fedpkg srpm
$ mock -r fedora-rawhide-x86_64 *.src.rpm
$ rpmlint -i ./*.spec /var/lib/mock/fedora-rawhide-x86_64/result/*.rpm

rebased onto 3fb5c63

4 years ago

jaruga commented 4 years ago

I rebased, and now this PR is ready for the review.

Dependency check: Is other packages using bowtie as BuildRequire or Require?: No. (OK)
License check: ok
rpmlint check: ok
Install check: ok
Running bowtie command on mock environment: ok
Scratch build: ok
https://koji.fedoraproject.org/koji/taskinfo?taskID=42047473

Running bowtie command on mock environment

I tested like this for installed bowite related commands.

$ scripts/test/simple_tests.pl --bowtie=/usr/bin/bowtie --bowtie-build=/usr/bin/bowtie-build

rebased onto 8f1cc3a

4 years ago

Pull-Request has been merged by jaruga

4 years ago

jaruga commented 4 years ago

Here is my working log.

Merge pull-request and build

$ git branch
* feature/update-to-v1.2.3
  master

$ fedpkg --release master srpm
setting SOURCE_DATE_EPOCH=1582848000
Wrote: /home/jaruga/git/fedora-packages/bowtie/bowtie-1.2.3-1.fc33.src.rpm

$ fedpkg import bowtie-1.2.3-1.fc33.src.rpm
...
diff --git a/sources b/sources
index d9f51b3..d91e553 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-8484fba71f78d94ee9e16a9b5c8c8d26  bowtie-1.0.1-src.zip
-83ecb7f17abdd274751ecc1dfc48cd4e  bowtie-arm-gcc.patch
+SHA512 (bowtie-1.2.3-tests.tgz) = 810120e7acc91cbc06dceba2387b921ada3644f63c3ffce4237fbb7edf317f8dba11d250e49dfb702ea3245dba27091f98bf3dec0b4c22b25e5b67fd2e78f5d3
+SHA512 (bowtie-src-x86_64.zip) = 3d902b8a060f1a6af41602c5169bea0b43a5d0f2f0c72286602dcd5f84c42f261d93acc05baa45a34a57fe9f2d223e3917b1aa29c7cb93d93f93b86a3f365174
...

$ cat sources
SHA512 (bowtie-1.2.3-tests.tgz) = 810120e7acc91cbc06dceba2387b921ada3644f63c3ffce4237fbb7edf317f8dba11d250e49dfb702ea3245dba27091f98bf3dec0b4c22b25e5b67fd2e78f5d3
SHA512 (bowtie-src-x86_64.zip) = 3d902b8a060f1a6af41602c5169bea0b43a5d0f2f0c72286602dcd5f84c42f261d93acc05baa45a34a57fe9f2d223e3917b1aa29c7cb93d93f93b86a3f365174

$ git status
On branch feature/update-to-v1.2.3
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
  modified:   .gitignore
  modified:   sources

Do commit with a dummy commit.

$ git commit -m 'Update'

Squash the 2 commits to 1 commit.

$ git rebase -i fc1b288290dc60df67e363d79bb9e268b5c85ce7

$ git remote -v
jaruga  ssh://jaruga@pkgs.fedoraproject.org/forks/jaruga/rpms/bowtie.git (fetch)
jaruga  ssh://jaruga@pkgs.fedoraproject.org/forks/jaruga/rpms/bowtie.git (push)
origin  ssh://jaruga@pkgs.fedoraproject.org/rpms/bowtie (fetch)
origin  ssh://jaruga@pkgs.fedoraproject.org/rpms/bowtie (push)

$ git push jaruga feature/update-to-v1.2.3 -f

Click "Merge" button at https://src.fedoraproject.org/rpms/bowtie/pull-request/1 .

Then

$ git checkout master

$ git pull

$ fedpkg build --nowait
Building bowtie-1.2.3-1.fc33 for rawhide
Created task: 42111413
Task info: https://koji.fedoraproject.org/koji/taskinfo?taskID=42111413