From 01090e63f3067303d6ca41e5bbea8b890bbab7b6 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Tue, 27 Dec 2022 01:06:46 +0100
Subject: sci-biology/bcftools: add 1.16

Signed-off-by: David Seifert <soap@gentoo.org>
---
 sci-biology/bcftools/Manifest             |  1 +
 sci-biology/bcftools/bcftools-1.16.ebuild | 42 +++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)
 create mode 100644 sci-biology/bcftools/bcftools-1.16.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 4dbacdb4a399..af5f3f40dd8b 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
+DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06 SHA512 998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3
diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild b/sci-biology/bcftools/bcftools-1.16.ebuild
new file mode 100644
index 000000000000..eeb9a7c890b7
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.16.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	dev-lang/perl
+	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+	=sci-libs/htslib-$(ver_cut 1-2)*:=
+	sys-libs/zlib
+	${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+	default
+
+	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--disable-bcftools-plugins \
+		--disable-libgsl \
+		--with-htslib=system
+}
-- 
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