diff options
author | bacon <bacon@pkgsrc.org> | 2021-12-17 15:25:20 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2021-12-17 15:25:20 +0000 |
commit | 3eb32ffa26e1b363d17899c864ebaa28b3da18c2 (patch) | |
tree | bcf28557684784afe87a9a62b313706b670b1dde /biology | |
parent | 64985d8fcbfb18d6f73b1a4ef8f5003c0b805ac3 (diff) | |
download | pkgsrc-3eb32ffa26e1b363d17899c864ebaa28b3da18c2.tar.gz |
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
Diffstat (limited to 'biology')
-rw-r--r-- | biology/bowtie2/Makefile | 10 | ||||
-rw-r--r-- | biology/bowtie2/PLIST | 2 | ||||
-rw-r--r-- | biology/bowtie2/distinfo | 10 | ||||
-rw-r--r-- | biology/bowtie2/patches/patch-Makefile | 10 | ||||
-rw-r--r-- | biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh | 2 |
5 files changed, 14 insertions, 20 deletions
diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index 63d0889d67d..3d61233c6d0 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -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 \ diff --git a/biology/bowtie2/PLIST b/biology/bowtie2/PLIST index 249ae7dddfe..b6bbb12d130 100644 --- a/biology/bowtie2/PLIST +++ b/biology/bowtie2/PLIST @@ -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 diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index bc405a9d3aa..6777f272847 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -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 diff --git a/biology/bowtie2/patches/patch-Makefile b/biology/bowtie2/patches/patch-Makefile index 23e15f3f6b9..aec17cfab1a 100644 --- a/biology/bowtie2/patches/patch-Makefile +++ b/biology/bowtie2/patches/patch-Makefile @@ -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 17:30:12 bacon Exp $ +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 $(SSE_FLAG) diff --git a/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh b/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh index 2a9ef93e68a..4cb5499da1f 100644 --- a/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh +++ b/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh @@ -1,4 +1,4 @@ -$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 |