From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id BF9D8158019 for ; Sun, 3 Oct 2021 17:41:50 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1EF92E088A; Sun, 3 Oct 2021 17:41:50 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-CHACHA20-POLY1305 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id CB7DAE088A for ; Sun, 3 Oct 2021 17:41:49 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-CHACHA20-POLY1305 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id F2A0B342F0A for ; Sun, 3 Oct 2021 17:41:48 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 90C45129 for ; Sun, 3 Oct 2021 17:41:47 +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: <1633282898.9eab85fba2bfef0ad9b849a75a7e78d2895d4eba.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-1.13.ebuild X-VCS-Directories: sci-biology/bcftools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 9eab85fba2bfef0ad9b849a75a7e78d2895d4eba X-VCS-Branch: master Date: Sun, 3 Oct 2021 17:41:47 +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: af144380-0143-4666-a095-cb2abe8a81e7 X-Archives-Hash: dafd27b889f2fa3386b4c3abcf54f38f commit: 9eab85fba2bfef0ad9b849a75a7e78d2895d4eba Author: David Seifert gentoo org> AuthorDate: Sun Oct 3 17:41:38 2021 +0000 Commit: David Seifert gentoo 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 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 +}