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# $NetBSD: Makefile,v 1.10 2021/03/20 18:17:07 bacon Exp $
DISTNAME= bcftools-1.12
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
MAINTAINER= bacon@NetBSD.org
HOMEPAGE= https://www.htslib.org/
COMMENT= Tools for manipulating BCF and VCF variant call files
LICENSE= mit
USE_TOOLS+= autoconf automake autoreconf bash gmake perl
GNU_CONFIGURE= yes
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
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/bsd.pkg.mk"
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