diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile index 0f6c3ba013e0..f66f21b9b81d 100644 --- a/biology/bcftools/Makefile +++ b/biology/bcftools/Makefile @@ -1,59 +1,59 @@ PORTNAME= bcftools -PORTVERSION= 1.16 +PORTVERSION= 1.17 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes USE_PERL5= test GH_ACCOUNT= samtools GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl OPTIONS_DEFINE= GPL GPL_DESC= Enable modules that rely on GPL code OPTIONS_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl .include .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 LICENSE+= GPLv3 LICENSE_COMB= multi .endif TEST_TARGET= test pre-configure: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ ${WRKSRC}/configure.ac post-install: ${MV} ${STAGEDIR}${PREFIX}/bin/color-chrs.pl \ ${STAGEDIR}${PREFIX}/bin/color-chrs ${MV} ${STAGEDIR}${PREFIX}/bin/guess-ploidy.py\ ${STAGEDIR}${PREFIX}/bin/guess-ploidy ${MV} /${STAGEDIR}${PREFIX}/bin/plot-roh.py \ ${STAGEDIR}${PREFIX}/bin/plot-roh ${MV} ${STAGEDIR}${PREFIX}/bin/run-roh.pl \ ${STAGEDIR}${PREFIX}/bin/run-roh ${MV} ${STAGEDIR}${PREFIX}/bin/vcfutils.pl \ ${STAGEDIR}${PREFIX}/bin/vcfutils ${MV} ${STAGEDIR}${PREFIX}/bin/plot-vcfstats \ ${STAGEDIR}${PREFIX}/bin/ .include diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo index 0ff5fb7eef59..e485c96d9038 100644 --- a/biology/bcftools/distinfo +++ b/biology/bcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1672094717 -SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3 -SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435 +TIMESTAMP = 1677246068 +SHA256 (samtools-bcftools-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e +SIZE (samtools-bcftools-1.17_GH0.tar.gz) = 3481344 diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist index 0a24964f9656..15a3206a846c 100644 --- a/biology/bcftools/pkg-plist +++ b/biology/bcftools/pkg-plist @@ -1,48 +1,49 @@ bin/bcftools bin/color-chrs bin/gff2gff.py bin/guess-ploidy bin/plot-roh bin/plot-vcfstats 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 libexec/bcftools/contrast.so libexec/bcftools/counts.so libexec/bcftools/dosage.so libexec/bcftools/fill-AN-AC.so libexec/bcftools/fill-from-fasta.so libexec/bcftools/fill-tags.so 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/mendelian2.so 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-dnm2.so libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so libexec/bcftools/variant-distance.so libexec/bcftools/variantkey-hex.so man/man1/bcftools.1.gz