biology/bowtie: Update to 1.3.1

Also adds support for aarch64 and powerpc64*

Changes:        https://github.com/BenLangmead/bowtie/tags

PR:             260389
Reported by:    pkubaj

6 files changed, 34 insertions, 80 deletions

diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile
index 5fb9ffdff3f0..10607fd8a77f 100644
--- a/biology/bowtie/Makefile
+++ b/biology/bowtie/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		bowtie
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.1.2
-PORTREVISION=		9
+DISTVERSION=		1.3.1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -9,21 +8,26 @@ COMMENT=	Ultrafast, memory-efficient short read aligner
 
 LICENSE=	ART10
 
-# May also work on other 64-bit platforms, but untested
-ONLY_FOR_ARCHS=	amd64
+ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le
 
-# FIXME: bowtie-align intermittently dumps core when compiled with clang
-# GCC 4.2 does not provide good performance
-USES=		gmake perl5 python:run shebangfix
-USE_GCC=	yes
+# c++11-lib is just for GCC 4.2-based systems
+# Remove it when support officially ends
+USES=		compiler:c++11-lib gmake perl5 python:run shebangfix
 USE_PERL5=	run
 USE_GITHUB=	yes
 
-SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build bowtie-inspect
+SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build scripts/bowtie-hbb.sh \
+		bowtie-inspect
 GH_ACCOUNT=	BenLangmead
 
 OPTIONS_DEFINE=	DOCS
 
+.include <bsd.port.options.mk>
+
+.if ${ARCH:Mpowerpc64*} || ${ARCH:Maarch64}
+MAKE_ENV=	POPCNT_CAPABILITY=0
+.endif
+
 post-install:
 	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_SCRIPT} \
diff --git a/biology/bowtie/distinfo b/biology/bowtie/distinfo
index ffacca889d6c..fbb7362c14e3 100644
--- a/biology/bowtie/distinfo
+++ b/biology/bowtie/distinfo
@@ -1,2 +1,3 @@
-SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7
-SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346
+TIMESTAMP = 1639406970
+SHA256 (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573
+SIZE (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 7672741
diff --git a/biology/bowtie/files/patch-Makefile b/biology/bowtie/files/patch-Makefile
index 8f3a35cf59f5..dcf2f7089076 100644
--- a/biology/bowtie/files/patch-Makefile
+++ b/biology/bowtie/files/patch-Makefile
@@ -1,52 +1,20 @@
---- Makefile.orig	2015-06-23 16:32:51 UTC
+--- Makefile.orig	2021-12-13 20:33:26 UTC
 +++ Makefile
-@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
- SEQAN_DIR = SeqAn-1.1
- SEQAN_INC = -I $(SEQAN_DIR)
- INC = $(SEQAN_INC) -I third_party
--CPP = g++
--CXX = $(CPP)
--CC = gcc
-+
-+# Use ?= to allow environment CPP, CC, CXX to take precedence.  This avoids
-+# the need to modify the Makefile on different platforms.  Package managers
-+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
-+CPP ?= g++
-+CXX ?= $(CPP)
-+CC ?= gcc
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 1
-@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
- PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
- 
- ifeq (1,$(WITH_TBB))
--	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
-+	LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
- 	EXTRA_FLAGS += -DWITH_TBB
- else
--	LIBS = $(PTHREAD_LIB)
-+	LIBS = ${LDFLAGS} $(PTHREAD_LIB)
+@@ -146,7 +146,7 @@ ifeq (32,$(BITS))
  endif
  
- SEARCH_LIBS = 
-@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
- VERSION = $(shell cat VERSION)
- 
- BITS=32
--ifeq (x86_64,$(shell uname -m))
-+ifeq (amd64,$(shell uname -m))
- 	BITS=64
- endif
- # msys will always be 32 bit so look at the cpu arch instead.
-@@ -143,8 +147,8 @@ ifeq (32,$(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 = -O
+ DEBUG_FLAGS = -O0 -g3
+-RELEASE_FLAGS = -O3
++RELEASE_FLAGS =
  NOASSERT_FLAGS = -DNDEBUG
  FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
  
+@@ -225,7 +225,7 @@ DEFS=-fno-strict-aliasing \
+      $(MM_DEF) \
+      $(SHMEM_DEF)
+ 
+-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
++ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS)
+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
+ 
diff --git a/biology/bowtie/files/patch-ebwt.h b/biology/bowtie/files/patch-ebwt.h
deleted file mode 100644
index 4272bbd8303c..000000000000
--- a/biology/bowtie/files/patch-ebwt.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- ebwt.h.orig	2018-11-03 20:51:56 UTC
-+++ ebwt.h
-@@ -860,7 +860,7 @@ public:
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	uint32_t*   isa() const          { return (uint32_t)_isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }
diff --git a/biology/bowtie/files/patch-processor__support.h b/biology/bowtie/files/patch-processor__support.h
deleted file mode 100644
index bbfecedb7a3b..000000000000
--- a/biology/bowtie/files/patch-processor__support.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- processor_support.h.orig	2020-07-04 10:42:26 UTC
-+++ processor_support.h
-@@ -49,7 +49,7 @@ class ProcessorSupport { (public)
- #elif defined(USING_GCC_COMPILER)
-         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
- #else
--        std::cerr << “ERROR: please define __cpuid() for this build.\n”; 
-+        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
-         assert(0);
- #endif
-         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
diff --git a/biology/bowtie/pkg-plist b/biology/bowtie/pkg-plist
index e0e8c2056459..0f6efe21b18c 100644
--- a/biology/bowtie/pkg-plist
+++ b/biology/bowtie/pkg-plist
@@ -26,7 +26,9 @@ bin/bowtie-inspect-s
 %%DATADIR%%/reads/e_coli_1000_1.fq
 %%DATADIR%%/reads/e_coli_1000_2.fa
 %%DATADIR%%/reads/e_coli_1000_2.fq
+%%DATADIR%%/reads/e_coli_1000_interleaved.fq
 %%DATADIR%%/scripts/best_verify.pl
+%%DATADIR%%/scripts/bowtie-hbb.sh
 %%DATADIR%%/scripts/bs_mapability.pl
 %%DATADIR%%/scripts/build_test.sh
 %%DATADIR%%/scripts/colorize_fasta.pl
@@ -58,6 +60,7 @@ bin/bowtie-inspect-s
 %%DATADIR%%/scripts/pe_verify.pl
 %%DATADIR%%/scripts/reconcile_alignments.pl
 %%DATADIR%%/scripts/reconcile_alignments_pe.pl
+%%DATADIR%%/scripts/run-hbb.sh
 %%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/manual.html
 %%PORTDOCS%%%%DOCSDIR%%/release.txt
@@ -81,7 +84,7 @@ bin/bowtie-inspect-s
 %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi
-%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh
+%%PORTDOCS%%%%DOCSDIR%%/website/push.sh
 %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi