diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index 92da7c61eff7..85603f8c1cc8 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -1,25 +1,27 @@ PORTNAME= samtools DISTVERSION= 1.17 +PORTREVISION= 1 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 USES= autoreconf gmake localbase ncurses perl5 python:env shebangfix USE_GITHUB= yes USE_PERL5= test GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl TEST_TARGET= test .include diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist index 15e146e410cd..2ef37918b44f 100644 --- a/biology/samtools/pkg-plist +++ b/biology/samtools/pkg-plist @@ -1,64 +1,64 @@ 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 bin/samtools 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-consensus.1.gz -man/man1/samtools-coverage.1.gz -man/man1/samtools-cram-size.1.gz -man/man1/samtools-depad.1.gz -man/man1/samtools-depth.1.gz -man/man1/samtools-dict.1.gz -man/man1/samtools-faidx.1.gz -man/man1/samtools-fasta.1.gz -man/man1/samtools-fastq.1.gz -man/man1/samtools-fixmate.1.gz -man/man1/samtools-flags.1.gz -man/man1/samtools-flagstat.1.gz -man/man1/samtools-fqidx.1.gz -man/man1/samtools-head.1.gz -man/man1/samtools-idxstats.1.gz -man/man1/samtools-import.1.gz -man/man1/samtools-index.1.gz -man/man1/samtools-markdup.1.gz -man/man1/samtools-merge.1.gz -man/man1/samtools-mpileup.1.gz -man/man1/samtools-phase.1.gz -man/man1/samtools-quickcheck.1.gz -man/man1/samtools-reference.1.gz -man/man1/samtools-reheader.1.gz -man/man1/samtools-reset.1.gz -man/man1/samtools-rmdup.1.gz -man/man1/samtools-samples.1.gz -man/man1/samtools-sort.1.gz -man/man1/samtools-split.1.gz -man/man1/samtools-stats.1.gz -man/man1/samtools-targetcut.1.gz -man/man1/samtools-tview.1.gz -man/man1/samtools-view.1.gz -man/man1/samtools.1.gz -man/man1/wgsim.1.gz +share/man/man1/samtools-addreplacerg.1.gz +share/man/man1/samtools-ampliconclip.1.gz +share/man/man1/samtools-ampliconstats.1.gz +share/man/man1/samtools-bedcov.1.gz +share/man/man1/samtools-calmd.1.gz +share/man/man1/samtools-cat.1.gz +share/man/man1/samtools-collate.1.gz +share/man/man1/samtools-consensus.1.gz +share/man/man1/samtools-coverage.1.gz +share/man/man1/samtools-cram-size.1.gz +share/man/man1/samtools-depad.1.gz +share/man/man1/samtools-depth.1.gz +share/man/man1/samtools-dict.1.gz +share/man/man1/samtools-faidx.1.gz +share/man/man1/samtools-fasta.1.gz +share/man/man1/samtools-fastq.1.gz +share/man/man1/samtools-fixmate.1.gz +share/man/man1/samtools-flags.1.gz +share/man/man1/samtools-flagstat.1.gz +share/man/man1/samtools-fqidx.1.gz +share/man/man1/samtools-head.1.gz +share/man/man1/samtools-idxstats.1.gz +share/man/man1/samtools-import.1.gz +share/man/man1/samtools-index.1.gz +share/man/man1/samtools-markdup.1.gz +share/man/man1/samtools-merge.1.gz +share/man/man1/samtools-mpileup.1.gz +share/man/man1/samtools-phase.1.gz +share/man/man1/samtools-quickcheck.1.gz +share/man/man1/samtools-reference.1.gz +share/man/man1/samtools-reheader.1.gz +share/man/man1/samtools-reset.1.gz +share/man/man1/samtools-rmdup.1.gz +share/man/man1/samtools-samples.1.gz +share/man/man1/samtools-sort.1.gz +share/man/man1/samtools-split.1.gz +share/man/man1/samtools-stats.1.gz +share/man/man1/samtools-targetcut.1.gz +share/man/man1/samtools-tview.1.gz +share/man/man1/samtools-view.1.gz +share/man/man1/samtools.1.gz +share/man/man1/wgsim.1.gz