bowtie2: Update to 2.4.4

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Dec 16 20:02:14 2021 -0600
Changeset:	c3c157dea76cbd22f470d1311b0bb76f313e7e6f

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

Log Message:
bowtie2: Update to 2.4.4

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c3c157dea76cbd22f470d1311b0bb76f313e7e6f

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

diffstat:
 bowtie2/Makefile               | 9 ++-------
 bowtie2/distinfo               | 8 ++++----
 bowtie2/patches/patch-Makefile | 8 ++++----
 3 files changed, 10 insertions(+), 15 deletions(-)

diffs:
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index ffe68b4764..b1aedd076b 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD$
 
-DISTNAME=	bowtie2-2.4.2
+DISTNAME=	bowtie2-2.4.4
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
@@ -16,17 +16,12 @@ REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
 REPLACE_SH=	scripts/bowtie2-hbb.sh
 
-# Use onetbb on supported platforms when a package is available
-MAKE_FLAGS+=	NO_TBB=1
-
 DATADIR=	${PREFIX}/share/bowtie2
 EXAMPLESDIR=	${PREFIX}/share/examples/bowtie2
 
-INSTALLATION_DIRS=	share/bowtie2/scripts share/examples/bowtie2
+INSTALLATION_DIRS=	bin share/bowtie2/scripts share/examples/bowtie2
 
 post-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bowtie2*-s ${WRKSRC}/bowtie2*-l \
-		${DESTDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/*.sh ${WRKSRC}/scripts/*.pl \
 		${DESTDIR}${DATADIR}/scripts
 	(cd ${WRKSRC}/example && pax -rw index reads reference \
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
index 19d3203d47..0180a42079 100644
--- a/bowtie2/distinfo
+++ b/bowtie2/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-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) = 00aa2794474478aa578f6aee5cdb319dfa132ae1
+BLAKE2s (bowtie2-2.4.4.tar.gz) = 685468ca08b60b58de8ed51fec3c7a22411c278f7e8c8703461707b4de996d3e
+SHA512 (bowtie2-2.4.4.tar.gz) = 2db44e8219bcb916119b8097dd10adcc2185d3ce7df6147210c78070dce57fefddbc79c64dc2a55fdc49a46c4df80c37c8c6d786cce20a95a2e50ce0692befed
+Size (bowtie2-2.4.4.tar.gz) = 10582238 bytes
+SHA1 (patch-Makefile) = 59b9823472a371fa9142a69b37df406c4ed47cd9
 SHA1 (patch-scripts_bowtie2-hbb.sh) = d360774cfef0675b4c1cdd1175b394d2cf7f761a
diff --git a/bowtie2/patches/patch-Makefile b/bowtie2/patches/patch-Makefile
index 3df5976ffa..218040ce96 100644
--- a/bowtie2/patches/patch-Makefile
+++ b/bowtie2/patches/patch-Makefile
@@ -1,8 +1,8 @@
 $NetBSD$
 
-# Respect PREFIX and CXXFLAGS
+# Respect pkgsrc env
 
---- Makefile.orig	2020-10-06 03:46:41.000000000 +0000
+--- Makefile.orig	2021-12-17 01:48:49.470438839 +0000
 +++ Makefile
 @@ -21,7 +21,7 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
@@ -12,8 +12,8 @@ $NetBSD$
 +PREFIX ?= /usr/local
  bindir := $(PREFIX)/bin
  
- ARCH := $(shell uname -m)
-@@ -234,7 +234,7 @@ ifeq (32,$(BITS))
+ LDLIBS := -lpthread -lz
+@@ -199,7 +199,7 @@ else ifeq (0,$(shell $(CXX) -E -fsanitiz
  endif
  
  DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)