[gentoo-commits] proj/sci:master commit in: sci-biology/polyphen/

["Andrew Ammerlaan" <andrewammerlaan@gentoo.org>]

commit:     98b76dd9389c5dfe59897373d568033c1999ab1e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:27:05 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> 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 <andrewammerlaan <AT> 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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>

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
-}