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 TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id AABB615808B for ; Sat, 19 Mar 2022 11:38:24 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id D51E22BC005; Sat, 19 Mar 2022 11:38:23 +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)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 80FC12BC001 for ; Sat, 19 Mar 2022 11:38:23 +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 5B8C93431AB for ; Sat, 19 Mar 2022 11:38:22 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 94E2C32E for ; Sat, 19 Mar 2022 11:38:20 +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: <1647689885.65bf4360727a6bceed339106305247eb0962f654.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-1.15.ebuild X-VCS-Directories: sci-biology/bcftools/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 65bf4360727a6bceed339106305247eb0962f654 X-VCS-Branch: master Date: Sat, 19 Mar 2022 11:38:20 +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: 60e8a570-72cd-4194-9101-77b5dd294d76 X-Archives-Hash: b420968b3904ecfa61faf867e5f3eb04 commit: 65bf4360727a6bceed339106305247eb0962f654 Author: David Seifert gentoo org> AuthorDate: Sat Mar 19 11:38:05 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Mar 19 11:38:05 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=65bf4360 sci-biology/bcftools: add 1.15 Signed-off-by: David Seifert gentoo.org> sci-biology/bcftools/Manifest | 1 + sci-biology/bcftools/bcftools-1.15.ebuild | 44 +++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index bfc2b78ed049..32704684a3cf 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1 +1,2 @@ DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb SHA512 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a +DIST bcftools-1.15.tar.bz2 6899394 BLAKE2B 44d11f5d594c547c0e3dfdcc9b2d8b55d837d17cf98465c4ce153ad0a8dce3db172276bdd24ad3dcecb3c9a064c649f3cbcc13e09194c2f655796e9a478cb27f SHA512 43fd7414c93175c6a8d69c8f8ba681a8c1f6b934ce0834dc130ff367825e60aa57736e36d379e5bdee84a01d018ee36eeeedebdbce85161745a5a063abdbca44 diff --git a/sci-biology/bcftools/bcftools-1.15.ebuild b/sci-biology/bcftools/bcftools-1.15.ebuild new file mode 100644 index 000000000000..4ec6b0a7e097 --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.15.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2022 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 +}