Received: by mail.netbsd.org (Postfix, from userid 605) id 9058C84D1C; Sat, 20 Mar 2021 18:17:10 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id C8D4F84CD8 for ; Sat, 20 Mar 2021 18:17:09 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id AOlT8i21T0IP for ; Sat, 20 Mar 2021 18:17:08 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 7C40684C13 for ; Sat, 20 Mar 2021 18:17:08 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 47E60FA95; Sat, 20 Mar 2021 18:17:08 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1616264228180010" MIME-Version: 1.0 Date: Sat, 20 Mar 2021 18:17:08 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20210320181708.47E60FA95@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1616264228180010 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sat Mar 20 18:17:08 UTC 2021 Modified Files: pkgsrc/biology/bcftools: Makefile PLIST distinfo pkgsrc/biology/bcftools/patches: patch-Makefile pkgsrc/biology/htslib: Makefile PLIST buildlink3.mk distinfo pkgsrc/biology/samtools: Makefile PLIST distinfo pkgsrc/biology/samtools/patches: patch-Makefile Removed Files: pkgsrc/biology/bcftools/patches: patch-misc_run-roh.pl pkgsrc/biology/htslib/patches: patch-Makefile patch-cram_open__trace__file.c patch-hfile__libcurl.c Log Message: biology/htslib: Update to 1.12 biology/bcftools: Update to 1.12 biology/samtools: Update to 1.12 Numerous enhancements, performance improvements, and bug fixes since 1.10 Minimized pkgsrc patches in all three packages Moved htslib to custom tarball since Github-generated distfiles are incomplete To generate a diff of this commit: cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/bcftools/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bcftools/PLIST \ pkgsrc/biology/bcftools/distinfo cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bcftools/patches/patch-Makefile cvs rdiff -u -r1.1 -r0 pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/htslib/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/htslib/PLIST cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/htslib/buildlink3.mk cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/htslib/distinfo cvs rdiff -u -r1.1 -r0 pkgsrc/biology/htslib/patches/patch-Makefile \ pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c \ pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/samtools/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/samtools/PLIST cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/samtools/distinfo cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/samtools/patches/patch-Makefile Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1616264228180010 Content-Disposition: inline Content-Length: 14011 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/bcftools/Makefile diff -u pkgsrc/biology/bcftools/Makefile:1.9 pkgsrc/biology/bcftools/Makefile:1.10 --- pkgsrc/biology/bcftools/Makefile:1.9 Fri Dec 4 20:45:00 2020 +++ pkgsrc/biology/bcftools/Makefile Sat Mar 20 18:17:07 2021 @@ -1,7 +1,6 @@ -# $NetBSD: Makefile,v 1.9 2020/12/04 20:45:00 nia Exp $ +# $NetBSD: Makefile,v 1.10 2021/03/20 18:17:07 bacon Exp $ -DISTNAME= bcftools-1.10.2 -PKGREVISION= 2 +DISTNAME= bcftools-1.12 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} Index: pkgsrc/biology/bcftools/PLIST diff -u pkgsrc/biology/bcftools/PLIST:1.2 pkgsrc/biology/bcftools/PLIST:1.3 --- pkgsrc/biology/bcftools/PLIST:1.2 Mon Jul 27 00:29:04 2020 +++ pkgsrc/biology/bcftools/PLIST Sat Mar 20 18:17:07 2021 @@ -1,6 +1,7 @@ -@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $ bin/bcftools bin/color-chrs +bin/gff2gff.py bin/guess-ploidy bin/plot-roh bin/plot-vcfstats @@ -34,12 +35,13 @@ libexec/bcftools/missing2ref.so libexec/bcftools/parental-origin.so libexec/bcftools/prune.so libexec/bcftools/remove-overlaps.so +libexec/bcftools/scatter.so libexec/bcftools/setGT.so 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 Index: pkgsrc/biology/bcftools/distinfo diff -u pkgsrc/biology/bcftools/distinfo:1.2 pkgsrc/biology/bcftools/distinfo:1.3 --- pkgsrc/biology/bcftools/distinfo:1.2 Mon Jul 27 00:29:04 2020 +++ pkgsrc/biology/bcftools/distinfo Sat Mar 20 18:17:07 2021 @@ -1,8 +1,7 @@ -$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $ +$NetBSD: distinfo,v 1.3 2021/03/20 18:17:07 bacon Exp $ -SHA1 (bcftools-1.10.2.tar.gz) = b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4 -RMD160 (bcftools-1.10.2.tar.gz) = 7713e8c5bd4195eb610544adb26158c16525fdac -SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f3dc259fbcc5c74b8dad3726b5f61efb57f0b8e3d0349577f7934240f36c82bd98849885a5593791995 -Size (bcftools-1.10.2.tar.gz) = 2880994 bytes -SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980 -SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659 +SHA1 (bcftools-1.12.tar.gz) = 17ded5a60da7a42d18fef5a846791ed295f69622 +RMD160 (bcftools-1.12.tar.gz) = 9d3a16c8266bcdd8f2a10f099aec3fc19da82a98 +SHA512 (bcftools-1.12.tar.gz) = f43074989a01cf4ef32a968935f5e5f3eacf2c04b9aa558d739166e3d96d3a498965d27db6482b2992b5d60fed3d2945ef3fd61fcc79b5dbe062994d49df4ad2 +Size (bcftools-1.12.tar.gz) = 3048508 bytes +SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731 Index: pkgsrc/biology/bcftools/patches/patch-Makefile diff -u pkgsrc/biology/bcftools/patches/patch-Makefile:1.1 pkgsrc/biology/bcftools/patches/patch-Makefile:1.2 --- pkgsrc/biology/bcftools/patches/patch-Makefile:1.1 Mon Jul 27 00:29:04 2020 +++ pkgsrc/biology/bcftools/patches/patch-Makefile Sat Mar 20 18:17:07 2021 @@ -1,49 +1,13 @@ -$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $ +$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $ # Respect pkgsrc env ---- Makefile.orig 2019-12-19 09:57:32.000000000 +0000 +--- Makefile.orig 2021-03-19 17:42:33.842623449 +0000 +++ Makefile -@@ -22,12 +22,12 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc --AR = ar --RANLIB = ranlib --CPPFLAGS = --CFLAGS = -g -Wall -O2 --LDFLAGS = -+CC ?= gcc -+AR ?= ar -+RANLIB ?= ranlib -+# CPPFLAGS = -+CFLAGS ?= -g -Wall -O2 -+# LDFLAGS = - LIBS = - - DYNAMIC_FLAGS = -rdynamic -@@ -45,12 +45,12 @@ 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 --exec_prefix = $(prefix) -+PREFIX ?= /usr/local -+exec_prefix = $(PREFIX) - bindir = $(exec_prefix)/bin - libdir = $(exec_prefix)/lib - libexecdir = $(exec_prefix)/libexec --mandir = $(prefix)/share/man -+mandir = $(PREFIX)/share/man - man1dir = $(mandir)/man1 - # Installation location for $(PLUGINS) - plugindir = $(libexecdir)/bcftools -@@ -59,12 +59,11 @@ pluginpath = $(plugindir) - misc_bindir = $(bindir) +@@ -60,11 +60,11 @@ misc_bindir = $(bindir) MKDIR_P = mkdir -p --INSTALL = install -p + INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -INSTALL_MAN = $(INSTALL_DATA) @@ -57,12 +21,3 @@ $NetBSD: patch-Makefile,v 1.1 2020/07/27 PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -78,7 +77,7 @@ TEST_PROGRAMS = test/test-rbuf test/test - - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(DL_LIBS) $(LIBS) -+ALL_LIBS = -lz $(LIBS) - - all: $(PROGRAMS) $(TEST_PROGRAMS) plugins - Index: pkgsrc/biology/htslib/Makefile diff -u pkgsrc/biology/htslib/Makefile:1.18 pkgsrc/biology/htslib/Makefile:1.19 --- pkgsrc/biology/htslib/Makefile:1.18 Mon Aug 31 18:06:39 2020 +++ pkgsrc/biology/htslib/Makefile Sat Mar 20 18:17:07 2021 @@ -1,9 +1,10 @@ -# $NetBSD: Makefile,v 1.18 2020/08/31 18:06:39 wiz Exp $ +# $NetBSD: Makefile,v 1.19 2021/03/20 18:17:07 bacon Exp $ -DISTNAME= htslib-1.10.2 -PKGREVISION= 2 +DISTNAME= htslib-1.12 CATEGORIES= biology -MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} +# Github-generated distfiles are incomplete, use custom tarballs instead +MASTER_SITES= https://github.com/samtools/htslib/releases/download/${PKGVERSION_NOREV}/ +EXTRACT_SUFX= .tar.bz2 MAINTAINER= bacon@NetBSD.org HOMEPAGE= https://www.htslib.org/ @@ -23,6 +24,7 @@ REPLACE_PERL+= test/*.pl CONFIGURE_ARGS+= --enable-libcurl PKGCONFIG_OVERRIDE= htslib.pc.in TEST_TARGET= test +MAKE_ENV+= BUILT_TEST_PROGRAMS='' pre-configure: cd ${WRKSRC} && autoreconf -if Index: pkgsrc/biology/htslib/PLIST diff -u pkgsrc/biology/htslib/PLIST:1.2 pkgsrc/biology/htslib/PLIST:1.3 --- pkgsrc/biology/htslib/PLIST:1.2 Wed Jul 22 14:50:14 2020 +++ pkgsrc/biology/htslib/PLIST Sat Mar 20 18:17:07 2021 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $ bin/bgzip bin/htsfile bin/tabix @@ -9,6 +9,7 @@ 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 @@ -17,6 +18,7 @@ include/htslib/khash.h include/htslib/khash_str2int.h include/htslib/klist.h include/htslib/knetfile.h +include/htslib/kroundup.h include/htslib/kseq.h include/htslib/ksort.h include/htslib/kstring.h Index: pkgsrc/biology/htslib/buildlink3.mk diff -u pkgsrc/biology/htslib/buildlink3.mk:1.4 pkgsrc/biology/htslib/buildlink3.mk:1.5 --- pkgsrc/biology/htslib/buildlink3.mk:1.4 Wed Jul 22 15:36:55 2020 +++ pkgsrc/biology/htslib/buildlink3.mk Sat Mar 20 18:17:07 2021 @@ -1,11 +1,11 @@ -# $NetBSD: buildlink3.mk,v 1.4 2020/07/22 15:36:55 bacon Exp $ +# $NetBSD: buildlink3.mk,v 1.5 2021/03/20 18:17:07 bacon Exp $ BUILDLINK_TREE+= htslib .if !defined(HTSLIB_BUILDLINK3_MK) HTSLIB_BUILDLINK3_MK:= -BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8 +BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2 BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.10.2 BUILDLINK_PKGSRCDIR.htslib?= ../../biology/htslib Index: pkgsrc/biology/htslib/distinfo diff -u pkgsrc/biology/htslib/distinfo:1.3 pkgsrc/biology/htslib/distinfo:1.4 --- pkgsrc/biology/htslib/distinfo:1.3 Wed Jul 22 14:50:14 2020 +++ pkgsrc/biology/htslib/distinfo Sat Mar 20 18:17:07 2021 @@ -1,9 +1,6 @@ -$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $ +$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $ -SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631 -RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6 -SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e -Size (htslib-1.10.2.tar.gz) = 1452177 bytes -SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911 -SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea -SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14 +SHA1 (htslib-1.12.tar.bz2) = 8cab518f97bbdf43165320c3a4bdef1e9a42893a +RMD160 (htslib-1.12.tar.bz2) = 3d93d91db8c382f42b8ad0843609cabd3b502b46 +SHA512 (htslib-1.12.tar.bz2) = a810c646561f5c8b3a19b73ac22ec5f25b04d4e88e1314988881a8120c54106591d1d65aa708bbe2608f0065ca8abe92bdd70ef59a0dd0cdf63ff45c10957092 +Size (htslib-1.12.tar.bz2) = 4094458 bytes Index: pkgsrc/biology/samtools/Makefile diff -u pkgsrc/biology/samtools/Makefile:1.10 pkgsrc/biology/samtools/Makefile:1.11 --- pkgsrc/biology/samtools/Makefile:1.10 Fri Dec 4 20:45:00 2020 +++ pkgsrc/biology/samtools/Makefile Sat Mar 20 18:17:07 2021 @@ -1,7 +1,6 @@ -# $NetBSD: Makefile,v 1.10 2020/12/04 20:45:00 nia Exp $ +# $NetBSD: Makefile,v 1.11 2021/03/20 18:17:07 bacon Exp $ -DISTNAME= samtools-1.10 -PKGREVISION= 2 +DISTNAME= samtools-1.12 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} @@ -26,7 +25,7 @@ SUBST_FILES.bash+= test/test.pl REPLACE_PERL+= misc/*.pl REPLACE_PERL+= test/*.pl -REPLACE_PERL+= misc/plot-bamstats +REPLACE_PERL+= misc/plot-bamstats misc/plot-ampliconstats REPLACE_LUA+= misc/*.lua CONFIGURE_ARGS+= --with-htslib=system Index: pkgsrc/biology/samtools/PLIST diff -u pkgsrc/biology/samtools/PLIST:1.2 pkgsrc/biology/samtools/PLIST:1.3 --- pkgsrc/biology/samtools/PLIST:1.2 Sun Jul 26 23:30:29 2020 +++ pkgsrc/biology/samtools/PLIST Sat Mar 20 18:17:07 2021 @@ -1,14 +1,16 @@ -@comment $NetBSD: PLIST,v 1.2 2020/07/26 23:30:29 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $ 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 bin/md5fa bin/md5sum-lite bin/novo2sam.pl +bin/plot-ampliconstats bin/plot-bamstats bin/psl2sam.pl bin/sam2vcf.pl @@ -20,10 +22,13 @@ bin/wgsim bin/wgsim_eval.pl bin/zoom2sam.pl man/man1/samtools-addreplacerg.1 +man/man1/samtools-ampliconclip.1 +man/man1/samtools-ampliconstats.1 man/man1/samtools-bedcov.1 man/man1/samtools-calmd.1 man/man1/samtools-cat.1 man/man1/samtools-collate.1 +man/man1/samtools-coverage.1 man/man1/samtools-depad.1 man/man1/samtools-depth.1 man/man1/samtools-dict.1 Index: pkgsrc/biology/samtools/distinfo diff -u pkgsrc/biology/samtools/distinfo:1.3 pkgsrc/biology/samtools/distinfo:1.4 --- pkgsrc/biology/samtools/distinfo:1.3 Sun Jul 26 23:30:29 2020 +++ pkgsrc/biology/samtools/distinfo Sat Mar 20 18:17:07 2021 @@ -1,7 +1,7 @@ -$NetBSD: distinfo,v 1.3 2020/07/26 23:30:29 bacon Exp $ +$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $ -SHA1 (samtools-1.10.tar.gz) = 98b24393629d63f2203f59c108b840b1e046f209 -RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007 -SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda -Size (samtools-1.10.tar.gz) = 4457760 bytes -SHA1 (patch-Makefile) = 409ef37ff0730257d82989d866c8cba705e3ef8a +SHA1 (samtools-1.12.tar.gz) = f46eb3a18885fb352d8746d51a206f7f34916232 +RMD160 (samtools-1.12.tar.gz) = 511ba541e9f3dbbab333d4a24a83f63c628b5b18 +SHA512 (samtools-1.12.tar.gz) = 7f468a4740610c2fdc42d8f020d3082e5b2b2e73b0c2dfc19b212ca259d703f34f7df0922e409a94500ccc0357d4d46306035be29c23a523ef6e959022f9d1db +Size (samtools-1.12.tar.gz) = 4528460 bytes +SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d Index: pkgsrc/biology/samtools/patches/patch-Makefile diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.1 pkgsrc/biology/samtools/patches/patch-Makefile:1.2 --- pkgsrc/biology/samtools/patches/patch-Makefile:1.1 Sun Jul 26 23:30:30 2020 +++ pkgsrc/biology/samtools/patches/patch-Makefile Sat Mar 20 18:17:07 2021 @@ -1,56 +1,24 @@ -$NetBSD: patch-Makefile,v 1.1 2020/07/26 23:30:30 bacon Exp $ +$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $ # Respect pkgsrc env ---- Makefile.orig 2020-07-21 20:20:56.996788479 +0000 +--- Makefile.orig 2021-03-19 17:48:34.572594186 +0000 +++ 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 -@@ -47,10 +47,10 @@ AOBJS= bam_index.o bam_plcmd.o sam_ - bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o - LZ4OBJS = $(LZ4DIR)/lz4.o - --prefix = /usr/local --exec_prefix = $(prefix) -+PREFIX ?= /usr/local -+exec_prefix = $(PREFIX) - bindir = $(exec_prefix)/bin --datarootdir = $(prefix)/share -+datarootdir = $(PREFIX)/share - mandir = $(datarootdir)/man - man1dir = $(mandir)/man1 - -@@ -58,12 +58,11 @@ man1dir = $(mandir)/man1 - misc_bindir = $(bindir) +@@ -61,12 +61,11 @@ misc_bindir = $(bindir) MKDIR_P = mkdir -p --INSTALL = install -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) +- +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 + --_----------=_1616264228180010--