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Bacon" Date: Sat, 20 Mar 2021 17:14:32 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r568874 - in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files X-SVN-Commit-Revision: 568874 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 20 Mar 2021 17:14:34 -0000 Author: jwb Date: Sat Mar 20 17:14:32 2021 New Revision: 568874 URL: https://svnweb.freebsd.org/changeset/ports/568874 Log: biology/htslib: Update to 1.12 biology/samtools: Update to 1.12 biology/bcftools: Update to 1.12 Numerous enhancements, performance improvements, and bug fixes since 1.11 Build-tested all other htslib dependents, no revbumps should be needed Reported by: portscout Deleted: head/biology/bcftools/files/patch-test_test.pl head/biology/bcftools/files/pkg-message.in head/biology/htslib/files/patch-hfile__libcurl.c head/biology/htslib/files/patch-sam.c head/biology/samtools/files/patch-test_test.pl Modified: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/files/patch-Makefile head/biology/bcftools/pkg-plist head/biology/htslib/Makefile head/biology/htslib/distinfo head/biology/htslib/files/patch-Makefile head/biology/htslib/pkg-plist head/biology/samtools/Makefile head/biology/samtools/distinfo head/biology/samtools/files/patch-Makefile head/biology/samtools/pkg-plist Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/bcftools/Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.11 +PORTVERSION= 1.12 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,14 +11,13 @@ COMMENT= Tools for manipulating next-generation sequen LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -LIB_DEPENDS= libhts.so.3:biology/htslib +LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes -USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} USE_PERL5= test GH_ACCOUNT= samtools Modified: head/biology/bcftools/distinfo ============================================================================== --- head/biology/bcftools/distinfo Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/bcftools/distinfo Sat Mar 20 17:14:32 2021 (r568874) @@ -1,3 +1,3 @@ -TIMESTAMP = 1603028344 -SHA256 (samtools-bcftools-1.11_GH0.tar.gz) = f2d9a09fd7920754b60948b81ec047882864213b93a0cd1ef0372b0e025cba3f -SIZE (samtools-bcftools-1.11_GH0.tar.gz) = 3004923 +TIMESTAMP = 1616112968 +SHA256 (samtools-bcftools-1.12_GH0.tar.gz) = b29e6d41ca0bb3f1761bee81be0c423329928a724a75501641c1ac5065d65526 +SIZE (samtools-bcftools-1.12_GH0.tar.gz) = 3048508 Modified: head/biology/bcftools/files/patch-Makefile ============================================================================== --- head/biology/bcftools/files/patch-Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/bcftools/files/patch-Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -1,16 +1,6 @@ ---- Makefile.orig 2020-10-18 13:31:52 UTC +--- Makefile.orig 2021-03-17 09:16:18 UTC +++ Makefile -@@ -45,7 +45,8 @@ OBJS = main.o vcfindex.o tabix.o \ - ccall.o em.o prob1.o kmin.o # the original samtools calling - PLUGIN_OBJS = vcfplugin.o - --prefix = /usr/local -+PREFIX ?= /usr/local -+prefix = $(PREFIX) - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin - libdir = $(exec_prefix)/lib -@@ -58,13 +59,14 @@ pluginpath = $(plugindir) +@@ -58,13 +58,14 @@ pluginpath = $(plugindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) @@ -32,7 +22,7 @@ PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -142,7 +144,7 @@ print-version: +@@ -142,7 +143,7 @@ print-version: ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o Modified: head/biology/bcftools/pkg-plist ============================================================================== --- head/biology/bcftools/pkg-plist Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/bcftools/pkg-plist Sat Mar 20 17:14:32 2021 (r568874) @@ -40,7 +40,7 @@ libexec/bcftools/smpl-stats.so libexec/bcftools/split-vep.so libexec/bcftools/split.so libexec/bcftools/tag2tag.so -libexec/bcftools/trio-dnm.so +libexec/bcftools/trio-dnm2.so libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so libexec/bcftools/variantkey-hex.so Modified: head/biology/htslib/Makefile ============================================================================== --- head/biology/htslib/Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/htslib/Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -2,8 +2,10 @@ # $FreeBSD$ PORTNAME= htslib -DISTVERSION= 1.11.0 +DISTVERSION= 1.12 CATEGORIES= biology devel +# Github generated distfiles are incomplete, so use custom tarball +MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= C library for high-throughput sequencing data formats @@ -15,12 +17,10 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libdeflate.so:archivers/libdeflate TEST_DEPENDS= bash:shells/bash -USES= autoreconf gmake localbase pathfix perl5 shebangfix -USE_GITHUB= yes +USES= autoreconf gmake localbase pathfix perl5 shebangfix tar:bzip2 USE_PERL5= test USE_LDCONFIG= yes -GH_ACCOUNT= samtools GNU_CONFIGURE= yes PATHFIX_MAKEFILEIN= Makefile SHEBANG_FILES= test/*.pl Modified: head/biology/htslib/distinfo ============================================================================== --- head/biology/htslib/distinfo Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/htslib/distinfo Sat Mar 20 17:14:32 2021 (r568874) @@ -1,3 +1,3 @@ -TIMESTAMP = 1602982298 -SHA256 (samtools-htslib-1.11.0_GH0.tar.gz) = 55356e78f25a20194488d94308335f409c3757101398961388caf38d3cce12dd -SIZE (samtools-htslib-1.11.0_GH0.tar.gz) = 1485848 +TIMESTAMP = 1616112272 +SHA256 (htslib-1.12.tar.bz2) = 2280141b46e953ba4ae01b98335a84f8e6ccbdb6d5cdbab7f70ee4f7e3b6f4ca +SIZE (htslib-1.12.tar.bz2) = 4094458 Modified: head/biology/htslib/files/patch-Makefile ============================================================================== --- head/biology/htslib/files/patch-Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/htslib/files/patch-Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -1,16 +1,6 @@ ---- Makefile.orig 2020-10-18 00:44:56 UTC +--- Makefile.orig 2021-03-20 15:53:14 UTC +++ Makefile -@@ -40,7 +40,8 @@ EXTRA_CFLAGS_PIC = -fpic - LDFLAGS = -fvisibility=hidden - LIBS = $(htslib_default_libs) - --prefix = /usr/local -+PREFIX ?= /usr/local -+prefix = $(PREFIX) - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin - includedir = $(prefix)/include -@@ -53,13 +54,14 @@ man5dir = $(mandir)/man5 +@@ -53,13 +53,14 @@ man5dir = $(mandir)/man5 man7dir = $(mandir)/man7 pkgconfigdir= $(prefix)/libdata/pkgconfig @@ -32,7 +22,7 @@ # Set by config.mk if plugins are enabled plugindir = -@@ -100,7 +102,7 @@ BUILT_THRASH_PROGRAMS = \ +@@ -102,7 +103,7 @@ BUILT_THRASH_PROGRAMS = \ test/thrash_threads6 \ test/thrash_threads7 @@ -40,4 +30,4 @@ +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \ htslib_static.mk htslib-uninstalled.pc - HTSPREFIX = + ALL_CPPFLAGS = -I. $(CPPFLAGS) Modified: head/biology/htslib/pkg-plist ============================================================================== --- head/biology/htslib/pkg-plist Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/htslib/pkg-plist Sat Mar 20 17:14:32 2021 (r568874) @@ -8,6 +8,7 @@ include/htslib/hfile.h include/htslib/hts.h include/htslib/hts_defs.h include/htslib/hts_endian.h +include/htslib/hts_expr.h include/htslib/hts_log.h include/htslib/hts_os.h include/htslib/kbitset.h @@ -30,7 +31,7 @@ include/htslib/vcf_sweep.h include/htslib/vcfutils.h lib/libhts.a lib/libhts.so -lib/libhts.so.1.11 +lib/libhts.so.%%PORTVERSION%% lib/libhts.so.3 libdata/pkgconfig/htslib.pc man/man1/bgzip.1.gz Modified: head/biology/samtools/Makefile ============================================================================== --- head/biology/samtools/Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/samtools/Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= samtools -DISTVERSION= 1.11 +DISTVERSION= 1.12 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,7 +11,7 @@ COMMENT= Tools for manipulating next-generation sequen LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -LIB_DEPENDS= libhts.so.3:biology/htslib +LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase ncurses perl5 python:env shebangfix Modified: head/biology/samtools/distinfo ============================================================================== --- head/biology/samtools/distinfo Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/samtools/distinfo Sat Mar 20 17:14:32 2021 (r568874) @@ -1,3 +1,3 @@ -TIMESTAMP = 1602982679 -SHA256 (samtools-samtools-1.11_GH0.tar.gz) = 80a54e93c5d111c15c005ee96a578bcd7e1bde34dba2242d981c539ff32f1738 -SIZE (samtools-samtools-1.11_GH0.tar.gz) = 4516328 +TIMESTAMP = 1616112844 +SHA256 (samtools-samtools-1.12_GH0.tar.gz) = a31695aca88b6acf52e1b579d84edb6b54f7b1b22227aad1ef6c6ccdd10314cf +SIZE (samtools-samtools-1.12_GH0.tar.gz) = 4528460 Modified: head/biology/samtools/files/patch-Makefile ============================================================================== --- head/biology/samtools/files/patch-Makefile Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/samtools/files/patch-Makefile Sat Mar 20 17:14:32 2021 (r568874) @@ -1,16 +1,6 @@ ---- Makefile.orig 2020-10-18 00:55:50 UTC +--- Makefile.orig 2021-03-17 09:14:26 UTC +++ Makefile -@@ -49,7 +49,8 @@ AOBJS= bam_index.o bam_plcmd.o sam_view.o bam_fas - bam_ampliconclip.o amplicon_stats.o - LZ4OBJS = $(LZ4DIR)/lz4.o - --prefix = /usr/local -+PREFIX ?= /usr/local -+prefix = $(PREFIX) - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin - datarootdir = $(prefix)/share -@@ -59,14 +60,14 @@ man1dir = $(mandir)/man1 +@@ -59,14 +59,14 @@ man1dir = $(mandir)/man1 # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) @@ -23,8 +13,8 @@ -INSTALL_SCRIPT = $(INSTALL_PROGRAM) - +# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set -+MKDIR_P = mkdir -p -+INSTALL = install -p ++MKDIR_P = mkdir -p ++INSTALL = install -p +INSTALL_DATA = ${BSD_INSTALL_DATA} +INSTALL_DIR = $(MKDIR_P) +INSTALL_MAN = ${BSD_INSTALL_MAN} Modified: head/biology/samtools/pkg-plist ============================================================================== --- head/biology/samtools/pkg-plist Sat Mar 20 15:59:49 2021 (r568873) +++ head/biology/samtools/pkg-plist Sat Mar 20 17:14:32 2021 (r568874) @@ -2,6 +2,7 @@ bin/ace2sam bin/blast2sam.pl bin/bowtie2sam.pl bin/export2sam.pl +bin/fasta-sanitize.pl bin/interpolate_sam.pl bin/maq2sam-long bin/maq2sam-short