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

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

commit:     688791dd334fa90d4d2a87015288141488db54b5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:26:56 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:26:56 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=688791dd

sci-biology/kraken: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/kraken/kraken-1.1.1-r2.ebuild | 51 ----------------------------
 sci-biology/kraken/kraken-2.1.1.ebuild    | 55 -------------------------------
 sci-biology/kraken/metadata.xml           | 12 -------
 3 files changed, 118 deletions(-)

diff --git a/sci-biology/kraken/kraken-1.1.1-r2.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild
deleted file mode 100644
index 3dd599b83..000000000
--- a/sci-biology/kraken/kraken-1.1.1-r2.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
-HOMEPAGE="https://ccb.jhu.edu/software/kraken"
-SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="1"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	net-misc/wget
-	sci-biology/jellyfish:1
-"
-
-src_prepare(){
-	default
-	sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die
-	echo "exit 0" >> install_kraken.sh || die
-}
-
-src_compile(){
-	./install_kraken.sh destdir || die
-}
-
-src_install(){
-	dodoc -r docs
-	perl_set_version
-	perl_domodule destdir/*.pm
-	dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm
-	insinto /usr/share/${PN}/util
-	doins destdir/*.pl
-	chmod -R a+rx "${ED}/usr/share/${PN}/util"
-	rm -f destdir/krakenlib.pm
-	dobin destdir/*
-}
-
-pkg_postinst(){
-	ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs"
-	ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read"
-	ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space"
-	ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM"
-	ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona"
-}

diff --git a/sci-biology/kraken/kraken-2.1.1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild
deleted file mode 100644
index 0991f94fa..000000000
--- a/sci-biology/kraken/kraken-2.1.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups"
-HOMEPAGE="https://ccb.jhu.edu/software/kraken2/"
-SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="2"
-KEYWORDS="~amd64"
-
-# TODO: somehow avoid the file conflict with kraken-1
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/ncbi-tools++
-	dev-lang/perl
-	net-misc/wget
-	!sci-biology/kraken:1
-"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-src_prepare(){
-	default
-	sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die
-	echo "exit 0" >> install_kraken2.sh || die
-}
-
-src_compile(){
-	./install_kraken2.sh destdir || die
-}
-
-src_install(){
-	dodoc -r docs
-	perl_set_version
-	perl_domodule destdir/*.pm
-	dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm
-	insinto /usr/share/${PN}/util
-	doins destdir/*.pl
-	chmod -R a+rx "${ED}/usr/share/${PN}/util"
-	rm -f destdir/krakenlib.pm
-	dobin destdir/*
-}
-
-pkg_postinst(){
-	ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs"
-	ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read"
-	ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space"
-	ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM"
-	ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona"
-}

diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/kraken/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>