commit: 9e53125a7a6ae8c74dc0b154c9f14498a4bbfb0d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 11:06:22 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 11:06:22 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e53125a
sci-biology/bcftools: add 1.19
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bcftools/Manifest | 1 +
sci-biology/bcftools/bcftools-1.19.ebuild | 42 +++++++++++++++++++++++++++++++
2 files changed, 43 insertions(+)
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 0f3c24a476a9..9cbcbdd02db5 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1 +1,2 @@
DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B
82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502
SHA512
39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68
+DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B
43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f
SHA512
a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746
diff --git a/sci-biology/bcftools/bcftools-1.19.ebuild
b/sci-biology/bcftools/bcftools-1.19.ebuild
new file mode 100644
index 000000000000..27d474fe35f9
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.19.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+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
+}
