From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id CB9D4158091 for ; Sun, 22 Jun 2025 15:33:42 +0000 (UTC) Received: from lists.gentoo.org (bobolink.gentoo.org [140.211.166.189]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange x25519) (No client certificate requested) (Authenticated sender: relay-lists.gentoo.org@gentoo.org) by smtp.gentoo.org (Postfix) with ESMTPSA id B1DD4341E66 for ; Sun, 22 Jun 2025 15:33:42 +0000 (UTC) Received: from bobolink.gentoo.org (localhost [127.0.0.1]) by bobolink.gentoo.org (Postfix) with ESMTP id F2BDA110527; Sun, 22 Jun 2025 15:33:37 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange x25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by bobolink.gentoo.org (Postfix) with ESMTPS id E88BA110527 for ; Sun, 22 Jun 2025 15:33:37 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange x25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A8E113417EE for ; Sun, 22 Jun 2025 15:33:37 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 15FEF22FC for ; Sun, 22 Jun 2025 15:33:36 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1750606393.a05f47085384c3ab44d448976fca34cd287554dc.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/bcftools/Manifest sci-biology/bcftools/bcftools-1.22.ebuild X-VCS-Directories: sci-biology/bcftools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: a05f47085384c3ab44d448976fca34cd287554dc X-VCS-Branch: master Date: Sun, 22 Jun 2025 15:33:36 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 64ec93a8-be23-4d68-9a7d-4cc22083dd43 X-Archives-Hash: 690716217b04123090a667eaf4077cf6 commit: a05f47085384c3ab44d448976fca34cd287554dc Author: David Seifert gentoo org> AuthorDate: Sun Jun 22 15:33:13 2025 +0000 Commit: David Seifert gentoo org> CommitDate: Sun Jun 22 15:33:13 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a05f4708 sci-biology/bcftools: add 1.22 Signed-off-by: David Seifert gentoo.org> sci-biology/bcftools/Manifest | 1 + sci-biology/bcftools/bcftools-1.22.ebuild | 42 +++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 05f6a8b2659e..079195ace32a 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,3 +1,4 @@ DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746 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-1.22.ebuild b/sci-biology/bcftools/bcftools-1.22.ebuild new file mode 100644 index 000000000000..9bc1805f0910 --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.22.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)*:= + 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 +}