Date: Thu, 05 Mar 2026 00:43:27 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: cde38c495ee7 - main - biology/bowtie2: Update to 2.5.5 Message-ID: <69a8d1af.1e61e.142677c5@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cde38c495ee712be66f9cb9da851234c34e7bcc2 commit cde38c495ee712be66f9cb9da851234c34e7bcc2 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2026-03-05 00:41:10 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2026-03-05 00:43:26 +0000 biology/bowtie2: Update to 2.5.5 Add -d (deterministic) flag for better efficiency Add runtime AVX detection on x86-64 Changes: https://github.com/BenLangmead/bowtie2/releases Reported by: portscout --- biology/bowtie2/Makefile | 15 +++++++++++++-- biology/bowtie2/distinfo | 6 +++--- biology/bowtie2/pkg-plist | 2 ++ 3 files changed, 18 insertions(+), 5 deletions(-) diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index 9ac09c497c50..90c2e22f7663 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -1,6 +1,6 @@ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.5.4 +DISTVERSION= 2.5.5 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org @@ -38,6 +38,14 @@ post-extract: MAKE_ENV= POPCNT_CAPABILITY=0 .endif +.include <bsd.port.pre.mk> + +.if ${ARCH} == amd64 +PLIST_SUB+= X86_64_ONLY="" +.else +PLIST_SUB+= X86_64_ONLY="@comment " +.endif + pre-configure: @${REINPLACE_CMD} \ -e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \ @@ -50,6 +58,9 @@ post-install: ${WRKSRC}/bowtie2*-s \ ${WRKSRC}/bowtie2*-l \ ${STAGEDIR}${PREFIX}/bin +.if ${ARCH} == amd64 + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*256 +.endif ${INSTALL_SCRIPT} \ ${WRKSRC}/scripts/*.sh \ ${WRKSRC}/scripts/*.pl \ @@ -62,4 +73,4 @@ post-install-DOCS-on: post-install-EXAMPLES-on: (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index c620003fbbce..367170fef258 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1716509204 -SHA256 (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13 -SIZE (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 10638569 +TIMESTAMP = 1771903062 +SHA256 (BenLangmead-bowtie2-v2.5.5_GH0.tar.gz) = e38d1833ec235ca27fa57589d32d897c9addf87085b7cb7bc978662954662da2 +SIZE (BenLangmead-bowtie2-v2.5.5_GH0.tar.gz) = 10645909 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743 diff --git a/biology/bowtie2/pkg-plist b/biology/bowtie2/pkg-plist index e79354fbbb9f..7ff259d16825 100644 --- a/biology/bowtie2/pkg-plist +++ b/biology/bowtie2/pkg-plist @@ -1,6 +1,8 @@ bin/bowtie2 bin/bowtie2-align-l +%%X86_64_ONLY%%bin/bowtie2-align-l-v256 bin/bowtie2-align-s +%%X86_64_ONLY%%bin/bowtie2-align-s-v256 bin/bowtie2-build bin/bowtie2-build-l bin/bowtie2-build-shome | help
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