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

[David Seifert]

commit:     20052cf2dfdc421aa1a194bf172703dd58ebbe06
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 10 12:41:48 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Jun 10 12:41:48 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20052cf2

sci-biology/bcftools: add 1.15.1

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

 sci-biology/bcftools/Manifest               |  1 +
 sci-biology/bcftools/bcftools-1.15.1.ebuild | 42 +++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 32704684a3cf..73403fe6ed42 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1,3 @@
 DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
+DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B 
d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731
 SHA512 
60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
 DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 
44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f
 SHA512 
43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44

diff --git a/sci-biology/bcftools/bcftools-1.15.1.ebuild 
b/sci-biology/bcftools/bcftools-1.15.1.ebuild
new file mode 100644
index 000000000000..7de00114bfa6
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.15.1.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..10} )
+
+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-${PV}*:=
+       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
+}