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Bacon" Subject: git: f488a27c4d56 - main - biology/bwa: Update to 0.7.18 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: f488a27c4d56bbdb72b779282ba86402d1699ca1 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f488a27c4d56bbdb72b779282ba86402d1699ca1 commit f488a27c4d56bbdb72b779282ba86402d1699ca1 Author: Jason W. Bacon AuthorDate: 2024-11-24 13:31:40 +0000 Commit: Jason W. Bacon CommitDate: 2024-11-24 13:31:40 +0000 biology/bwa: Update to 0.7.18 Official support for aarch64 (we already had this patched in) A few minor enhancements and fixes Changes: https://github.com/lh3/bwa/releases PR: 282923 Reported by: alster@vinterdalen.se --- biology/bwa/Makefile | 26 ++++++++++---------------- biology/bwa/distinfo | 8 +++----- biology/bwa/files/patch-ksw.c | 12 ++++++------ biology/bwa/pkg-descr | 18 +++++++++++++++--- 4 files changed, 34 insertions(+), 30 deletions(-) diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index eef1e1a5948d..11d77f255875 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -1,35 +1,29 @@ PORTNAME= bwa -PORTVERSION= 0.7.17 -DISTVERSIONPREFIX=v -PORTREVISION= 2 +DISTVERSIONPREFIX= v +DISTVERSION= 0.7.18 CATEGORIES= biology -PATCH_SITES= https://github.com/lh3/bwa/commit/ -PATCHFILES= 2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch:-p1 - MAINTAINER= jwb@FreeBSD.org COMMENT= Burrows-Wheeler sequence aligner -WWW= https://sourceforge.net/projects/bio-bwa/ +WWW= https://github.com/lh3/bwa/ LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN_mips= fails to compile: cc1: unrecognized command line option "-msse2" -BROKEN_mips64= fails to compile: cc1: unrecognized command line option "-msse2" +# Recheck these after 0.7.18 update +BROKEN_mips= fails to compile: cc1: unrecognized command line option "-msse2" +BROKEN_mips64= fails to compile: cc1: unrecognized command line option "-msse2" BUILD_DEPENDS= simde>0:devel/simde USES= gmake localbase perl5 shebangfix tar:bzip2 -SHEBANG_FILES= qualfa2fq.pl xa2multi.pl -USE_PERL5= run - USE_GITHUB= yes GH_ACCOUNT= lh3 +USE_PERL5= run -PLIST_FILES= bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl share/man/man1/bwa.1.gz +SHEBANG_FILES= qualfa2fq.pl xa2multi.pl -# Avoid #error in emmintrin.h -CFLAGS_i386= -msse2 -CFLAGS_amd64= -msse2 +PLIST_FILES= bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl share/man/man1/bwa.1.gz do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo index e4f099c0700c..b9b0548bf588 100644 --- a/biology/bwa/distinfo +++ b/biology/bwa/distinfo @@ -1,5 +1,3 @@ -TIMESTAMP = 1598613295 -SHA256 (lh3-bwa-v0.7.17_GH0.tar.gz) = 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd -SIZE (lh3-bwa-v0.7.17_GH0.tar.gz) = 232593 -SHA256 (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 15216a79759a2390bda4a4684af34ff3108f63519d2ec3935754507f3c008da0 -SIZE (2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch) = 709 +TIMESTAMP = 1732300398 +SHA256 (lh3-bwa-v0.7.18_GH0.tar.gz) = 194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870 +SIZE (lh3-bwa-v0.7.18_GH0.tar.gz) = 238036 diff --git a/biology/bwa/files/patch-ksw.c b/biology/bwa/files/patch-ksw.c index c86cabf2e497..f5314cbe72ce 100644 --- a/biology/bwa/files/patch-ksw.c +++ b/biology/bwa/files/patch-ksw.c @@ -1,13 +1,13 @@ ---- ksw.c.orig 2021-12-01 13:48:35 UTC +--- ksw.c.orig 2024-11-22 18:42:53 UTC +++ ksw.c -@@ -26,7 +26,9 @@ - #include +@@ -27,7 +27,9 @@ #include #include + #if defined __SSE2__ -#include +// #include +#define SIMDE_ENABLE_NATIVE_ALIASES +#include - #include "ksw.h" - - #ifdef USE_MALLOC_WRAPPERS + #elif defined __ARM_NEON + #include "neon_sse.h" + #else diff --git a/biology/bwa/pkg-descr b/biology/bwa/pkg-descr index 60f539b01220..e0c3d83a0b28 100644 --- a/biology/bwa/pkg-descr +++ b/biology/bwa/pkg-descr @@ -1,3 +1,15 @@ -BWA is a program for aligning sequencing reads against a large reference -genome (e.g. human genome). It has two major components, one for read shorter -than 150bp and the other for longer reads. +BWA is a software package for mapping DNA sequences against a large +reference genome, such as the human genome. It consists of three +algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is +designed for Illumina sequence reads up to 100bp, while the other two +are for longer sequences ranging from 70bp to a few megabases. BWA-MEM +and BWA-SW share similar features such as the support of long reads +and chimeric alignment, but BWA-MEM, which is the latest, is generally +recommended, as it is faster and more accurate. BWA-MEM also has +better performance than BWA-backtrack for 70-100bp Illumina reads. + +For all algorithms, BWA first needs to construct the FM-index for the +reference genome (the "bwa index" command). Alignment algorithms are +invoked with different sub-commands: "bwa aln/samse/sampe" for +BWA-backtrack, "bwa bwasw" for BWA-SW, and "bwa mem" for the BWA-MEM +algorithm.