bowtie2: Upgrade to 2.4.2 and clean up

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 20 18:40:57 2021 -0600
Changeset:	04e2f69daee84f6ef6d482ba514fd8b083cf2fe6

Modified Files:
	bowtie2/Makefile
	bowtie2/PLIST
	bowtie2/distinfo
	bowtie2/patches/patch-Makefile

Log Message:
bowtie2: Upgrade to 2.4.2 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=04e2f69daee84f6ef6d482ba514fd8b083cf2fe6

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bowtie2/Makefile               | 31 +++++++++++++------------------
 bowtie2/PLIST                  |  2 ++
 bowtie2/distinfo               | 10 +++++-----
 bowtie2/patches/patch-Makefile | 24 +++++++-----------------
 4 files changed, 27 insertions(+), 40 deletions(-)

diffs:
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index ea71d0a67d..31c523f504 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -5,23 +5,24 @@
 #              Wed Mar  2 08:06:07 CST 2016               #
 ###########################################################
 
-DISTNAME=	bowtie2-${PV}
+DISTNAME=	bowtie2-2.4.2
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
-GITHUB_PROJECT=	bowtie2
-GITHUB_TAG=	v${PV}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://bowtie-bio.sourceforge.net/index.shtml
+HOMEPAGE=	https://github.com/BenLangmead/bowtie2
 COMMENT=	Ultrafast, memory-efficient short read aligner
-LICENSE=	artistic
+LICENSE=	gnu-gpl-v3
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake perl:run pax
 REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
 
-PV=		2.3.4.2
+# TBB is a little challenging, so use pthreads until onetbb is committed
+MAKE_FLAGS+=	NO_TBB=1
+
 DATADIR=	${PREFIX}/share/bowtie2
 DOCSDIR=	${PREFIX}/share/doc/bowtie2
 EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
@@ -29,22 +30,16 @@ EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
 INSTALLATION_DIRS=	share/bowtie2/scripts
 
 post-install:
-	${INSTALL_PROGRAM} \
-		${WRKSRC}/bowtie2*-s \
-		${WRKSRC}/bowtie2*-l \
+	${INSTALL_PROGRAM} ${WRKSRC}/bowtie2*-s ${WRKSRC}/bowtie2*-l \
 		${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} \
-		${WRKSRC}/scripts/*.sh \
-		${WRKSRC}/scripts/*.pl \
+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/*.sh ${WRKSRC}/scripts/*.pl \
 		${DESTDIR}${DATADIR}/scripts
-	${INSTALL_SCRIPT} \
-		${FILESDIR}/bowtie2-manual \
+	${INSTALL_SCRIPT} ${FILESDIR}/bowtie2-manual \
 		${DESTDIR}${PREFIX}/bin
-	cd ${WRKSRC}/example && pax -rw index reads reference \
-		${DESTDIR}${EXAMPLESDIR}
-	cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR}
+	(cd ${WRKSRC}/example && pax -rw index reads reference \
+		${DESTDIR}${EXAMPLESDIR})
+	(cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR})
 
 .include "../../lang/python/application.mk"
-.include "../../wip/tbb/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bowtie2/PLIST b/bowtie2/PLIST
index ad6020b631..71aaa407f1 100644
--- a/bowtie2/PLIST
+++ b/bowtie2/PLIST
@@ -9,6 +9,7 @@ bin/bowtie2-inspect
 bin/bowtie2-inspect-l
 bin/bowtie2-inspect-s
 bin/bowtie2-manual
+share/bowtie2/scripts/bowtie2-hbb.sh
 share/bowtie2/scripts/convert_quals.pl
 share/bowtie2/scripts/gen_2b_occ_lookup.pl
 share/bowtie2/scripts/gen_occ_lookup.pl
@@ -59,6 +60,7 @@ share/examples/bowtie2/index/lambda_virus.4.bt2
 share/examples/bowtie2/index/lambda_virus.rev.1.bt2
 share/examples/bowtie2/index/lambda_virus.rev.2.bt2
 share/examples/bowtie2/reads/combined_reads.bam
+share/examples/bowtie2/reads/conversion_utilities.sh
 share/examples/bowtie2/reads/longreads.fq
 share/examples/bowtie2/reads/reads_1.fq
 share/examples/bowtie2/reads/reads_2.fq
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
index ea43eee4f8..492bc07979 100644
--- a/bowtie2/distinfo
+++ b/bowtie2/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-SHA1 (bowtie2-2.3.4.2.tar.gz) = 492434eac513cc480902b9ded2f3e70f0887f100
-RMD160 (bowtie2-2.3.4.2.tar.gz) = 582f4518db7a2eeb9178a404747586c2eb5b408b
-SHA512 (bowtie2-2.3.4.2.tar.gz) = eeb12569f3af9b45c702f47cf72e765cb060865365745e29a884b14df4ada33cf7d0b25f9e1c2680c12cbc0ab84d9d14b0910e53f992613508ede00edf14611e
-Size (bowtie2-2.3.4.2.tar.gz) = 10571530 bytes
-SHA1 (patch-Makefile) = 9b229a672d083deeb1be2ba8a42bcf342eb301c9
+SHA1 (bowtie2-2.4.2.tar.gz) = b8eb8158828459412586003b6051d79ed123fc82
+RMD160 (bowtie2-2.4.2.tar.gz) = 0c6c5fe29a40f913e3810d1fe022b948403dfb09
+SHA512 (bowtie2-2.4.2.tar.gz) = f8bb74aaec7557bcd1bc4b5ec5e2a3b141d78c88b04f39cdcc417d15f058bdb48b15d159c4ab569b4d655e3d1bd0cf8152343f05b9a20d5d29680c3e8c2f1a05
+Size (bowtie2-2.4.2.tar.gz) = 10590144 bytes
+SHA1 (patch-Makefile) = 041f35da8bccdf6d7c3bfe4306992e04b6a7c516
diff --git a/bowtie2/patches/patch-Makefile b/bowtie2/patches/patch-Makefile
index dac0ce9a9e..8f72363b20 100644
--- a/bowtie2/patches/patch-Makefile
+++ b/bowtie2/patches/patch-Makefile
@@ -1,25 +1,15 @@
 $NetBSD$
 
-# Respect env
---- Makefile.orig	2018-09-14 16:46:59.124139009 +0000
+# Respect PREFIX
+
+--- Makefile.orig	2021-01-21 00:03:29.754913712 +0000
 +++ Makefile
-@@ -21,8 +21,8 @@
+@@ -21,7 +21,7 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
  #
  
--prefix := /usr/local
--bindir := $(prefix)/bin
+-PREFIX := /usr/local
 +PREFIX ?= /usr/local
-+bindir := $(PREFIX)/bin
- 
- LDLIBS := -lz
- GCC_PREFIX := $(shell dirname `which gcc`)
-@@ -187,7 +187,7 @@ endif
- SSE_FLAG := -msse2
+ bindir := $(PREFIX)/bin
  
- DEBUG_FLAGS    := -O0 -g3 -m64 $(SSE_FLAG)
--RELEASE_FLAGS  := -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
-+RELEASE_FLAGS  := $(CXXFLAGS)
- NOASSERT_FLAGS := -DNDEBUG
- FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
+ ARCH := $(shell uname -m)