[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/

[David Seifert]

commit:     44c2c0b7d6006ee664863ccaf60bbde18a7a2153
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:11:00 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:11:00 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c2c0b7

sci-biology/bcftools: add 1.17

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/bcftools/Manifest             |  1 +
 sci-biology/bcftools/bcftools-1.17.ebuild | 42 +++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 2302cb589b4f..8d5aa1eec079 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 
0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06
 SHA512 
998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3
+DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 
82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502
 SHA512 
39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68

diff --git a/sci-biology/bcftools/bcftools-1.17.ebuild 
b/sci-biology/bcftools/bcftools-1.17.ebuild
new file mode 100644
index 000000000000..6adee705bb46
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.17.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..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
+}