CVS commit: pkgsrc/biology/bowtie2

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Dec 17 15:25:20 UTC 2021

Modified Files:
        pkgsrc/biology/bowtie2: Makefile PLIST distinfo
        pkgsrc/biology/bowtie2/patches: patch-Makefile
            patch-scripts_bowtie2-hbb.sh

Log Message:
biology/bowtie2: Update to 2.4.4

Replaced TBB with C++ threads
Support for Apple M1
Several other fixes and enhancements

Changes: https://github.com/BenLangmead/bowtie2/tags


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bowtie2/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bowtie2/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/bowtie2/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bowtie2/patches/patch-Makefile \
    pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh

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

Modified files:

Index: pkgsrc/biology/bowtie2/Makefile
diff -u pkgsrc/biology/bowtie2/Makefile:1.2 pkgsrc/biology/bowtie2/Makefile:1.3
--- pkgsrc/biology/bowtie2/Makefile:1.2 Mon May 24 19:49:10 2021
+++ pkgsrc/biology/bowtie2/Makefile     Fri Dec 17 15:25:20 2021
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.2 2021/05/24 19:49:10 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2021/12/17 15:25:20 bacon Exp $
 
-DISTNAME=      bowtie2-2.4.2
-PKGREVISION=   1
+DISTNAME=      bowtie2-2.4.4
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=BenLangmead/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -17,17 +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
 
 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 \

Index: pkgsrc/biology/bowtie2/PLIST
diff -u pkgsrc/biology/bowtie2/PLIST:1.1 pkgsrc/biology/bowtie2/PLIST:1.2
--- pkgsrc/biology/bowtie2/PLIST:1.1    Thu Jan 21 17:30:12 2021
+++ pkgsrc/biology/bowtie2/PLIST        Fri Dec 17 15:25:20 2021
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2021/01/21 17:30:12 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/12/17 15:25:20 bacon Exp $
 bin/bowtie2
 bin/bowtie2-align-l
 bin/bowtie2-align-s

Index: pkgsrc/biology/bowtie2/distinfo
diff -u pkgsrc/biology/bowtie2/distinfo:1.3 pkgsrc/biology/bowtie2/distinfo:1.4
--- pkgsrc/biology/bowtie2/distinfo:1.3 Tue Oct 26 10:03:37 2021
+++ pkgsrc/biology/bowtie2/distinfo     Fri Dec 17 15:25:20 2021
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:37 nia Exp $
+$NetBSD: distinfo,v 1.4 2021/12/17 15:25:20 bacon Exp $
 
-BLAKE2s (bowtie2-2.4.2.tar.gz) = bcd37b47ac9c639ae58ec8e5acbdd034520c6a7c80eaad29d0d0c20e580206e3
-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

Index: pkgsrc/biology/bowtie2/patches/patch-Makefile
diff -u pkgsrc/biology/bowtie2/patches/patch-Makefile:1.1 pkgsrc/biology/bowtie2/patches/patch-Makefile:1.2
--- pkgsrc/biology/bowtie2/patches/patch-Makefile:1.1   Thu Jan 21 17:30:12 2021
+++ pkgsrc/biology/bowtie2/patches/patch-Makefile       Fri Dec 17 15:25:20 2021
@@ -1,8 +1,8 @@
-$NetBSD: patch-Makefile,v 1.1 2021/01/21 17:30:12 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/12/17 15:25:20 bacon Exp $
 
-# 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: patch-Makefile,v 1.1 2021/01/21
 +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 $(SSE_FLAG)
Index: pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
diff -u pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.1 pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.2
--- pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh:1.1     Thu Jan 21 17:30:12 2021
+++ pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Fri Dec 17 15:25:20 2021
@@ -1,4 +1,4 @@
-$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.1 2021/01/21 17:30:12 bacon Exp $
+$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.2 2021/12/17 15:25:20 bacon Exp $
 
 # Eliminate bash dependency