Date: Thu, 5 Nov 2020 20:32:40 +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: r554156 - in head/biology/samtools: . files Message-ID: <202011052032.0A5KWe5Y037739@repo.freebsd.org>
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Author: jwb Date: Thu Nov 5 20:32:39 2020 New Revision: 554156 URL: https://svnweb.freebsd.org/changeset/ports/554156 Log: biology/samtools: Upgrade to 1.11 Numerous new features, bug fixes and performance enhancements https://github.com/samtools/samtools/releases/tag/1.11 Reported by: portscout Deleted: head/biology/samtools/files/pkg-message.in Modified: head/biology/samtools/Makefile head/biology/samtools/distinfo head/biology/samtools/files/patch-Makefile head/biology/samtools/pkg-plist Modified: head/biology/samtools/Makefile ============================================================================== --- head/biology/samtools/Makefile Thu Nov 5 20:30:50 2020 (r554155) +++ head/biology/samtools/Makefile Thu Nov 5 20:32:39 2020 (r554156) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= samtools -DISTVERSION= 1.10 +DISTVERSION= 1.11 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -20,7 +20,6 @@ USE_GITHUB= yes USE_PERL5= test GNU_CONFIGURE= yes -SUB_FILES= pkg-message SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl TEST_TARGET= test Modified: head/biology/samtools/distinfo ============================================================================== --- head/biology/samtools/distinfo Thu Nov 5 20:30:50 2020 (r554155) +++ head/biology/samtools/distinfo Thu Nov 5 20:32:39 2020 (r554156) @@ -1,3 +1,3 @@ -TIMESTAMP = 1595117115 -SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9 -SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760 +TIMESTAMP = 1602982679 +SHA256 (samtools-samtools-1.11_GH0.tar.gz) = 80a54e93c5d111c15c005ee96a578bcd7e1bde34dba2242d981c539ff32f1738 +SIZE (samtools-samtools-1.11_GH0.tar.gz) = 4516328 Modified: head/biology/samtools/files/patch-Makefile ============================================================================== --- head/biology/samtools/files/patch-Makefile Thu Nov 5 20:30:50 2020 (r554155) +++ head/biology/samtools/files/patch-Makefile Thu Nov 5 20:32:39 2020 (r554156) @@ -1,25 +1,7 @@ ---- Makefile.orig 2019-12-06 16:40:42 UTC +--- Makefile.orig 2020-10-18 00:55:50 UTC +++ Makefile -@@ -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 +@@ -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 @@ -28,27 +10,26 @@ exec_prefix = $(prefix) bindir = $(exec_prefix)/bin datarootdir = $(prefix)/share --mandir = $(datarootdir)/man -+mandir = $(prefix)/man - man1dir = $(mandir)/man1 - +@@ -59,14 +60,14 @@ man1dir = $(mandir)/man1 # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) --misc_bindir = $(bindir) -+misc_bindir = $(bindir)/samtools_misc + misc_bindir = $(bindir) -+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set - MKDIR_P = mkdir -p +-MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -INSTALL_SCRIPT = $(INSTALL_PROGRAM) +- ++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set ++MKDIR_P = mkdir -p ++INSTALL = install -p +INSTALL_DATA = ${BSD_INSTALL_DATA} +INSTALL_DIR = $(MKDIR_P) +INSTALL_MAN = ${BSD_INSTALL_MAN} +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} +INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} - PROGRAMS = samtools + Modified: head/biology/samtools/pkg-plist ============================================================================== --- head/biology/samtools/pkg-plist Thu Nov 5 20:30:50 2020 (r554155) +++ head/biology/samtools/pkg-plist Thu Nov 5 20:32:39 2020 (r554156) @@ -1,28 +1,32 @@ +bin/ace2sam +bin/blast2sam.pl +bin/bowtie2sam.pl +bin/export2sam.pl +bin/interpolate_sam.pl +bin/maq2sam-long +bin/maq2sam-short +bin/md5fa +bin/md5sum-lite +bin/novo2sam.pl +bin/plot-ampliconstats +bin/plot-bamstats +bin/psl2sam.pl +bin/sam2vcf.pl bin/samtools -bin/samtools_misc/ace2sam -bin/samtools_misc/blast2sam.pl -bin/samtools_misc/bowtie2sam.pl -bin/samtools_misc/export2sam.pl -bin/samtools_misc/interpolate_sam.pl -bin/samtools_misc/maq2sam-long -bin/samtools_misc/maq2sam-short -bin/samtools_misc/md5fa -bin/samtools_misc/md5sum-lite -bin/samtools_misc/novo2sam.pl -bin/samtools_misc/plot-bamstats -bin/samtools_misc/psl2sam.pl -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/wgsim -bin/samtools_misc/wgsim_eval.pl -bin/samtools_misc/zoom2sam.pl +bin/samtools.pl +bin/seq_cache_populate.pl +bin/soap2sam.pl +bin/wgsim +bin/wgsim_eval.pl +bin/zoom2sam.pl man/man1/samtools-addreplacerg.1.gz +man/man1/samtools-ampliconclip.1.gz +man/man1/samtools-ampliconstats.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-coverage.1.gz man/man1/samtools-depad.1.gz man/man1/samtools-depth.1.gz man/man1/samtools-dict.1.gz
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