Date: Mon, 3 Aug 2020 18:22:06 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r544098 - in head/biology/samtools: . files Message-ID: <202008031822.073IM67A063953@repo.freebsd.org>
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Author: jwb Date: Mon Aug 3 18:22:06 2020 New Revision: 544098 URL: https://svnweb.freebsd.org/changeset/ports/544098 Log: biology/samtools: Upgrade to 1.10 Numerous bug fixes and enhancements: https://github.com/samtools/samtools/releases/tag/1.10 Take maintainership per ports/248089 PR: ports/248089 Modified: head/biology/samtools/Makefile head/biology/samtools/distinfo (contents, props changed) head/biology/samtools/files/patch-Makefile (contents, props changed) head/biology/samtools/files/patch-test_test.pl head/biology/samtools/pkg-plist (contents, props changed) Modified: head/biology/samtools/Makefile ============================================================================== --- head/biology/samtools/Makefile Mon Aug 3 18:21:18 2020 (r544097) +++ head/biology/samtools/Makefile Mon Aug 3 18:22:06 2020 (r544098) @@ -2,29 +2,26 @@ # $FreeBSD$ PORTNAME= samtools -DISTVERSION= 1.9 -PORTREVISION= 1 +DISTVERSION= 1.10 CATEGORIES= biology -MAINTAINER= cartwright@asu.edu +MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= htslib>=1.6:biology/htslib -LIB_DEPENDS= libhts.so:biology/htslib +LIB_DEPENDS= libhts.so.3:biology/htslib TEST_DEPENDS= bash:shells/bash -USES= autoreconf gmake localbase ncurses \ - perl5 python:env shebangfix +USES= autoreconf gmake localbase ncurses perl5 python:env shebangfix USE_GITHUB= yes USE_PERL5= test GNU_CONFIGURE= yes SUB_FILES= pkg-message -SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl +SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl TEST_TARGET= test Modified: head/biology/samtools/distinfo ============================================================================== --- head/biology/samtools/distinfo Mon Aug 3 18:21:18 2020 (r544097) +++ head/biology/samtools/distinfo Mon Aug 3 18:22:06 2020 (r544098) @@ -1,3 +1,3 @@ -TIMESTAMP = 1532906637 -SHA256 (samtools-samtools-1.9_GH0.tar.gz) = 211600bd180d01030b3fe25baa7ae1c105106bed6c3f8d993f41dd278d44c637 -SIZE (samtools-samtools-1.9_GH0.tar.gz) = 4098992 +TIMESTAMP = 1595117115 +SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9 +SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760 Modified: head/biology/samtools/files/patch-Makefile ============================================================================== --- head/biology/samtools/files/patch-Makefile Mon Aug 3 18:21:18 2020 (r544097) +++ head/biology/samtools/files/patch-Makefile Mon Aug 3 18:22:06 2020 (r544098) @@ -1,11 +1,30 @@ ---- Makefile.orig 2017-09-28 11:12:01 UTC +--- Makefile.orig 2019-12-06 16:40:42 UTC +++ Makefile -@@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o bam_markdup.o +@@ -21,12 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. +-CC = gcc +-AR = ar +-CPPFLAGS = ++CC ?= gcc ++AR ?= ar ++# CPPFLAGS = + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 +-CFLAGS = -g -Wall -O2 +-LDFLAGS = ++CFLAGS ?= -g -Wall -O2 ++# LDFLAGS = + LIBS = + + LZ4DIR = ./lz4 +@@ -47,23 +47,24 @@ AOBJS= bam_index.o bam_plcmd.o sam_view.o bam_fas + bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o + LZ4OBJS = $(LZ4DIR)/lz4.o + -prefix = /usr/local -+prefix = ${PREFIX} ++PREFIX ?= /usr/local ++prefix = $(PREFIX) exec_prefix = $(prefix) bindir = $(exec_prefix)/bin datarootdir = $(prefix)/share @@ -17,6 +36,7 @@ -misc_bindir = $(bindir) +misc_bindir = $(bindir)/samtools_misc ++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 Modified: head/biology/samtools/files/patch-test_test.pl ============================================================================== --- head/biology/samtools/files/patch-test_test.pl Mon Aug 3 18:21:18 2020 (r544097) +++ head/biology/samtools/files/patch-test_test.pl Mon Aug 3 18:22:06 2020 (r544098) @@ -1,20 +1,20 @@ ---- test/test.pl.orig 2017-10-18 06:08:39 UTC +--- test/test.pl.orig 2020-07-21 20:48:50 UTC +++ test/test.pl -@@ -636,7 +636,7 @@ sub test_usage +@@ -907,7 +907,7 @@ sub test_usage my $command = $args{cmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}"); - if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; } -+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; } ++ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; } my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); -@@ -694,7 +694,7 @@ sub test_usage_subcommand +@@ -965,7 +965,7 @@ sub test_usage_subcommand my $commandpath = $$opts{bin}."/".$command; my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}"); - if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; } -+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; } ++ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; } if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; } Modified: head/biology/samtools/pkg-plist ============================================================================== --- head/biology/samtools/pkg-plist Mon Aug 3 18:21:18 2020 (r544097) +++ head/biology/samtools/pkg-plist Mon Aug 3 18:22:06 2020 (r544098) @@ -15,9 +15,38 @@ bin/samtools_misc/sam2vcf.pl bin/samtools_misc/samtools.pl bin/samtools_misc/seq_cache_populate.pl bin/samtools_misc/soap2sam.pl -bin/samtools_misc/varfilter.py bin/samtools_misc/wgsim bin/samtools_misc/wgsim_eval.pl bin/samtools_misc/zoom2sam.pl +man/man1/samtools-addreplacerg.1.gz +man/man1/samtools-bedcov.1.gz +man/man1/samtools-calmd.1.gz +man/man1/samtools-cat.1.gz +man/man1/samtools-collate.1.gz +man/man1/samtools-depad.1.gz +man/man1/samtools-depth.1.gz +man/man1/samtools-dict.1.gz +man/man1/samtools-faidx.1.gz +man/man1/samtools-fasta.1.gz +man/man1/samtools-fastq.1.gz +man/man1/samtools-fixmate.1.gz +man/man1/samtools-flags.1.gz +man/man1/samtools-flagstat.1.gz +man/man1/samtools-fqidx.1.gz +man/man1/samtools-idxstats.1.gz +man/man1/samtools-index.1.gz +man/man1/samtools-markdup.1.gz +man/man1/samtools-merge.1.gz +man/man1/samtools-mpileup.1.gz +man/man1/samtools-phase.1.gz +man/man1/samtools-quickcheck.1.gz +man/man1/samtools-reheader.1.gz +man/man1/samtools-rmdup.1.gz +man/man1/samtools-sort.1.gz +man/man1/samtools-split.1.gz +man/man1/samtools-stats.1.gz +man/man1/samtools-targetcut.1.gz +man/man1/samtools-tview.1.gz +man/man1/samtools-view.1.gz man/man1/samtools.1.gz man/man1/wgsim.1.gz
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