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

[David Seifert]

commit:     abdd260168c6e08cf711889889e7b258a85b3a56
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 29 13:40:20 2025 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Nov 29 13:40:20 2025 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=abdd2601

sci-biology/bcftools: bring back 1.21 for pysam

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

 sci-biology/bcftools/Manifest             |  1 +
 sci-biology/bcftools/bcftools-1.21.ebuild | 42 +++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index d3a406dd029a..1432031b9576 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,2 +1,3 @@
 DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 
36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17
 SHA512 
c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a
+DIST bcftools-1.21.tar.bz2 7982173 BLAKE2B 
7da808d1b06d2cdc0ed9ae2768a71f9e3e1de07f6e9c74504eb6f19b06481e509630e14f209ec0250c0689bf9d5807936288ba48f17830a2b004b7cfa3c23c59
 SHA512 
f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
 DIST bcftools-1.22.tar.bz2 8176878 BLAKE2B 
62df4b50e8ee6d4e9614f9317a58a72cc75adf89329cf2759f0e2b65027c51cbb4728e60128b22b4786e2ec541433664f3d7af5d70611dd32d362d2be7f56d0e
 SHA512 
20daee4ecb6b7d0034e0d9590fcc42712ac78c4e511d519ac0dd98d2b2b920d85d234cf1a08abd1be62d1be994788de53d6010af642099f2b75753ecc19efd15

diff --git a/sci-biology/bcftools/bcftools-1.21.ebuild 
b/sci-biology/bcftools/bcftools-1.21.ebuild
new file mode 100644
index 000000000000..866c1af6cee2
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.21.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{11..13} )
+
+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)*:=
+       virtual/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
+}