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

["David Seifert" <soap@gentoo.org>]

commit:     fbdda699ffc5db18d5dc0b5e2c59cf511dec93b5
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  3 16:54:26 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug  3 16:54:26 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fbdda699

sci-biology/bcftools: Bump to version 1.10.2

Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/bcftools/Manifest               |  1 +
 sci-biology/bcftools/bcftools-1.10.2.ebuild | 43 +++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index eef8daed7a7..508a5c41fe3 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1,3 @@
+DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
 DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
 DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c

diff --git a/sci-biology/bcftools/bcftools-1.10.2.ebuild b/sci-biology/bcftools/bcftools-1.10.2.ebuild
new file mode 100644
index 00000000000..179f7dea77e
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.10.2.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+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_MULTI_USEDEP}]
+	')
+	=sci-libs/htslib-${PV}*:=
+	sys-libs/zlib:=
+	${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+
+	python_fix_shebang misc/{guess-ploidy,plot-roh}.py
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--disable-bcftools-plugins \
+		--disable-libgsl \
+		--with-htslib=system
+}