Received: by mail.netbsd.org (Postfix, from userid 605) id 693DA84DFF; Mon, 27 Jul 2020 00:29:06 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id D90EA84CDA for ; Mon, 27 Jul 2020 00:29:05 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id Py5v8Hs6RoNx for ; Mon, 27 Jul 2020 00:29:04 +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 CE0E384E08 for ; Mon, 27 Jul 2020 00:29:04 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id BB2B9FB28; Mon, 27 Jul 2020 00:29:04 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1595809744126100" MIME-Version: 1.0 Date: Mon, 27 Jul 2020 00:29:04 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/bcftools To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20200727002904.BB2B9FB28@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1595809744126100 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Mon Jul 27 00:29:04 UTC 2020 Modified Files: pkgsrc/biology/bcftools: DESCR Makefile PLIST distinfo Added Files: pkgsrc/biology/bcftools/patches: patch-Makefile patch-misc_run-roh.pl Log Message: biology/bcftools: Upgrade to 1.10.2 Numerous bug fixes, usability improvements and sanity checks were added since 1.9 to prevent common user errors. To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bcftools/DESCR \ pkgsrc/biology/bcftools/PLIST pkgsrc/biology/bcftools/distinfo cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/bcftools/Makefile cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bcftools/patches/patch-Makefile \ pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1595809744126100 Content-Disposition: inline Content-Length: 10005 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/bcftools/DESCR diff -u pkgsrc/biology/bcftools/DESCR:1.1 pkgsrc/biology/bcftools/DESCR:1.2 --- pkgsrc/biology/bcftools/DESCR:1.1 Thu Nov 15 09:21:24 2018 +++ pkgsrc/biology/bcftools/DESCR Mon Jul 27 00:29:04 2020 @@ -1,11 +1,4 @@ -BCFtools is a program for variant calling and manipulating files in the Variant -Call Format (VCF) and its binary counterpart BCF. All commands work -transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. -In order to avoid tedious repetion, throughout this document we will use "VCF" -and "BCF" interchangeably, unless specifically noted. - -Most commands accept VCF, bgzipped VCF and BCF with filetype detected -automatically even when streaming from a pipe. Indexed VCF and BCF work in all -situations. Unindexed VCF and BCF and streams work in most, but not all -situations. In general, whenever multiple VCFs are read simultaneously, they -must be indexed and therefore also compressed. +BCFtools is a set of utilities that manipulate variant calls in the +Variant Call Format (VCF) and its binary counterpart BCF. All +commands work transparently with both VCFs and BCFs, both +uncompressed and BGZF-compressed. Index: pkgsrc/biology/bcftools/PLIST diff -u pkgsrc/biology/bcftools/PLIST:1.1 pkgsrc/biology/bcftools/PLIST:1.2 --- pkgsrc/biology/bcftools/PLIST:1.1 Thu Nov 15 09:21:24 2018 +++ pkgsrc/biology/bcftools/PLIST Mon Jul 27 00:29:04 2020 @@ -1,15 +1,17 @@ -@comment $NetBSD: PLIST,v 1.1 2018/11/15 09:21:24 adam Exp $ +@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $ bin/bcftools -bin/color-chrs.pl -bin/guess-ploidy.py -bin/plot-roh.py +bin/color-chrs +bin/guess-ploidy +bin/plot-roh bin/plot-vcfstats -bin/run-roh.pl -bin/vcfutils.pl +bin/run-roh +bin/vcfutils libexec/bcftools/GTisec.so libexec/bcftools/GTsubset.so libexec/bcftools/ad-bias.so +libexec/bcftools/add-variantkey.so libexec/bcftools/af-dist.so +libexec/bcftools/allele-length.so libexec/bcftools/check-ploidy.so libexec/bcftools/check-sparsity.so libexec/bcftools/color-chrs.so @@ -23,15 +25,22 @@ libexec/bcftools/fixploidy.so libexec/bcftools/fixref.so libexec/bcftools/frameshifts.so libexec/bcftools/guess-ploidy.so +libexec/bcftools/gvcfz.so libexec/bcftools/impute-info.so +libexec/bcftools/indel-stats.so libexec/bcftools/isecGT.so libexec/bcftools/mendelian.so libexec/bcftools/missing2ref.so +libexec/bcftools/parental-origin.so libexec/bcftools/prune.so +libexec/bcftools/remove-overlaps.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-stats.so libexec/bcftools/trio-switch-rate.so +libexec/bcftools/variantkey-hex.so man/man1/bcftools.1 Index: pkgsrc/biology/bcftools/distinfo diff -u pkgsrc/biology/bcftools/distinfo:1.1 pkgsrc/biology/bcftools/distinfo:1.2 --- pkgsrc/biology/bcftools/distinfo:1.1 Thu Nov 15 09:21:24 2018 +++ pkgsrc/biology/bcftools/distinfo Mon Jul 27 00:29:04 2020 @@ -1,6 +1,8 @@ -$NetBSD: distinfo,v 1.1 2018/11/15 09:21:24 adam Exp $ +$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $ -SHA1 (bcftools-1.9.tar.bz2) = 9b649c3f407528ee193210f68b8e21e8b0aebf31 -RMD160 (bcftools-1.9.tar.bz2) = 59b9997aaa509ba84c41b7e78821f31eca8d90dc -SHA512 (bcftools-1.9.tar.bz2) = fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c -Size (bcftools-1.9.tar.bz2) = 3134355 bytes +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 Index: pkgsrc/biology/bcftools/Makefile diff -u pkgsrc/biology/bcftools/Makefile:1.6 pkgsrc/biology/bcftools/Makefile:1.7 --- pkgsrc/biology/bcftools/Makefile:1.6 Sat Jan 18 23:30:08 2020 +++ pkgsrc/biology/bcftools/Makefile Mon Jul 27 00:29:04 2020 @@ -1,30 +1,55 @@ -# $NetBSD: Makefile,v 1.6 2020/01/18 23:30:08 rillig Exp $ +# $NetBSD: Makefile,v 1.7 2020/07/27 00:29:04 bacon Exp $ -DISTNAME= bcftools-1.9 -PKGREVISION= 2 +DISTNAME= bcftools-1.10.2 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} -EXTRACT_SUFX= .tar.bz2 -GITHUB_RELEASE= ${PKGVERSION_NOREV} MAINTAINER= bacon@NetBSD.org -HOMEPAGE= https://samtools.github.io/bcftools/ -COMMENT= Calling and manipulating files VCF and BCF formats +HOMEPAGE= https://www.htslib.org/ +COMMENT= Tools for manipulating BCF and VCF variant call files LICENSE= mit -USE_TOOLS+= gmake perl -GNU_CONFIGURE= yes -CONFIGURE_ARGS+= --with-htslib=system -TEST_TARGET= test +USE_TOOLS+= autoconf automake autoreconf bash gmake perl +GNU_CONFIGURE= yes -BUILDLINK_TRANSFORM+= opt:-ldl:${BUILDLINK_LDADD.dl:M*} +SUBST_CLASSES+= version +SUBST_STAGE.version= pre-configure +SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|" +SUBST_FILES.version= configure.ac + +SUBST_CLASSES+= bash +SUBST_STAGE.bash= pre-configure +SUBST_SED.bash+= -e 's|/bin/bash|${TOOLS_PATH.bash}|' +SUBST_SED.bash+= -e 's|\\/bin\\/bash|${TOOLS_PATH.bash:S,/,\\\/,g}|' +SUBST_FILES.bash= test/test.pl REPLACE_PERL+= misc/*.pl +REPLACE_PERL+= misc/fix-broken-GATK-Double-vs-Integer REPLACE_PERL+= misc/plot-vcfstats +REPLACE_PERL+= test/test.pl REPLACE_PYTHON+= misc/*.py -.include "../../devel/zlib/buildlink3.mk" +CONFIGURE_ARGS+= --with-htslib=system +MAKE_ENV+= USE_GPL=1 +TEST_TARGET= test + +pre-configure: + cd ${WRKSRC} && autoreconf -if + +post-install: + ${MV} ${DESTDIR}${PREFIX}/bin/color-chrs.pl \ + ${DESTDIR}${PREFIX}/bin/color-chrs + ${MV} ${DESTDIR}${PREFIX}/bin/guess-ploidy.py\ + ${DESTDIR}${PREFIX}/bin/guess-ploidy + ${MV} ${DESTDIR}${PREFIX}/bin/plot-roh.py \ + ${DESTDIR}${PREFIX}/bin/plot-roh + ${MV} ${DESTDIR}${PREFIX}/bin/run-roh.pl \ + ${DESTDIR}${PREFIX}/bin/run-roh + ${MV} ${DESTDIR}${PREFIX}/bin/vcfutils.pl \ + ${DESTDIR}${PREFIX}/bin/vcfutils + +BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2 .include "../../biology/htslib/buildlink3.mk" +.include "../../devel/zlib/buildlink3.mk" .include "../../lang/python/application.mk" -.include "../../mk/dlopen.buildlink3.mk" .include "../../mk/bsd.pkg.mk" Added files: Index: pkgsrc/biology/bcftools/patches/patch-Makefile diff -u /dev/null pkgsrc/biology/bcftools/patches/patch-Makefile:1.1 --- /dev/null Mon Jul 27 00:29:04 2020 +++ pkgsrc/biology/bcftools/patches/patch-Makefile Mon Jul 27 00:29:04 2020 @@ -0,0 +1,68 @@ +$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $ + +# Respect pkgsrc env + +--- Makefile.orig 2019-12-19 09:57:32.000000000 +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) + + 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) ++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 = 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) $(TEST_PROGRAMS) plugins + Index: pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl diff -u /dev/null pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl:1.1 --- /dev/null Mon Jul 27 00:29:04 2020 +++ pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl Mon Jul 27 00:29:04 2020 @@ -0,0 +1,24 @@ +$NetBSD: patch-misc_run-roh.pl,v 1.1 2020/07/27 00:29:04 bacon Exp $ + +# bash path + +--- misc/run-roh.pl.orig 2019-12-19 09:57:32.000000000 +0000 ++++ misc/run-roh.pl +@@ -110,7 +110,7 @@ sub cmd + + if ( $args{verbose} ) { print STDERR $cmd,"\n"; } + +- # Why not to use backticks? Perl calls /bin/sh, which is often bash. To get the correct ++ # Why not to use backticks? Perl calls bash, which is often bash. To get the correct + # status of failing pipes, it must be called with the pipefail option. + + my $kid_io; +@@ -127,7 +127,7 @@ sub cmd + else + { + # child +- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!"); ++ exec('bash', '-c', $cmd) or error("Failed to run the command [bash -c $cmd]: $!"); + } + + if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; } --_----------=_1595809744126100--