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

[David Seifert]

commit:     9eab85fba2bfef0ad9b849a75a7e78d2895d4eba
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct  3 17:41:38 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct  3 17:41:38 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9eab85fb

sci-biology/bcftools: add 1.13

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

 sci-biology/bcftools/Manifest             |  1 +
 sci-biology/bcftools/bcftools-1.13.ebuild | 44 +++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 77114df86c0..958ce72a852 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
 DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 
51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e
 SHA512 
f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
+DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 
4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb
 SHA512 
aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a

diff --git a/sci-biology/bcftools/bcftools-1.13.ebuild 
b/sci-biology/bcftools/bcftools-1.13.ebuild
new file mode 100644
index 00000000000..b0ddd23857c
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.13.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2021 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
+}