biology/samtools: import samtools-1.8

Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

OK wiz@


(bacon)

Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

# $NetBSD: Makefile,v 1.1 2018/05/07 18:37:31 bacon Exp $

DISTNAME=	samtools-1.8
CATEGORIES=	biology
MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
GITHUB_TAG=	${PKGVERSION_NOREV}

MAINTAINER=	bacon@NetBSD.org
HOMEPAGE=	http://www.htslib.org/
COMMENT=	Tools for manipulating next-generation sequencing data
LICENSE=	mit

USE_TOOLS+=	autoconf automake autoreconf gmake perl:run
GNU_CONFIGURE=	yes
REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
REPLACE_PYTHON=	misc/*.py

pre-configure:
	cd ${WRKSRC} && autoreconf

.include "../../mk/curses.buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../biology/htslib/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

@comment $NetBSD: PLIST,v 1.1 2018/05/07 18:37:31 bacon Exp $
bin/ace2sam
bin/blast2sam.pl
bin/bowtie2sam.pl
bin/export2sam.pl
bin/interpolate_sam.pl
bin/maq2sam-long
bin/maq2sam-short
bin/md5fa
bin/md5sum-lite
bin/novo2sam.pl
bin/plot-bamstats
bin/psl2sam.pl
bin/sam2vcf.pl
bin/samtools
bin/samtools.pl
bin/seq_cache_populate.pl
bin/soap2sam.pl
bin/varfilter.py
bin/wgsim
bin/wgsim_eval.pl
bin/zoom2sam.pl
man/man1/samtools.1
man/man1/wgsim.1

$NetBSD: distinfo,v 1.1 2018/05/07 18:37:31 bacon Exp $

SHA1 (samtools-1.8.tar.gz) = 5ac70ba4c324c223398ab4c0689933564985303c
RMD160 (samtools-1.8.tar.gz) = 47e4fde82a686669322fd330374aa37b148b7954
SHA512 (samtools-1.8.tar.gz) = 82e4d5f855f944cc989902154a99eada2b4c81939bd936fa1d471cf9ff01e03c8a7f773928ae55ef691f2827aa4076126678940bb89a322fa56d83c517677d0c
Size (samtools-1.8.tar.gz) = 4047378 bytes