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 AA74C15ACFC for ; Tue, 2 May 2023 12:27:32 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EC1C2E08B1; Tue, 2 May 2023 12:27:31 +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 D0A44E08B1 for ; Tue, 2 May 2023 12:27:31 +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)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id E61D9340FE5 for ; Tue, 2 May 2023 12:27:30 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 84971A5C for ; Tue, 2 May 2023 12:27:29 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1683030425.98b76dd9389c5dfe59897373d568033c1999ab1e.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/polyphen/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/polyphen/metadata.xml sci-biology/polyphen/polyphen-2.2.2.ebuild X-VCS-Directories: sci-biology/polyphen/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 98b76dd9389c5dfe59897373d568033c1999ab1e X-VCS-Branch: master Date: Tue, 2 May 2023 12:27:29 +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: de5e5cdf-4dcc-483a-89af-775fc23774bb X-Archives-Hash: 8e405fa6b07934acc6fde972719a1a5b commit: 98b76dd9389c5dfe59897373d568033c1999ab1e Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:27:05 2023 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:27:05 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=98b76dd9 sci-biology/polyphen: treeclean Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/polyphen/metadata.xml | 12 ------- sci-biology/polyphen/polyphen-2.2.2.ebuild | 56 ------------------------------ 2 files changed, 68 deletions(-) diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/polyphen/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biology@gentoo.org - Gentoo Biology Project - - diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild deleted file mode 100644 index 3100c6bbd..000000000 --- a/sci-biology/polyphen/polyphen-2.2.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Predict effect of aminoacid substitution on human protein function" -HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start" -SRC_URI=" - http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz - http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz - http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip -" - -LICENSE="polyphen" # for non-commercial use only -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-perl/CGI - sci-biology/ncbi-blast+ -" -RDEPEND="${DEPEND}" -BDEPEND="app-arch/unzip" - -# 3.7GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2 - -# 2.4GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2 - -# 895MB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2 - -src_unpack() { - unpack "polyphen-${PV}r405d.tar.gz" - cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die - cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die -} - -src_configure() { - # non-standard configure script - ./configure -} - -src_compile() { - pushd src - emake -j1 - popd -} - -src_install() { - pushd src - default - popd - einstalldocs -}