sci-biology/augustus: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>

3 files changed, 0 insertions, 128 deletions

diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
deleted file mode 100644
index 10dd2ad82..000000000
--- a/sci-biology/augustus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST augustus-3.3.2.tar.gz 235794642 BLAKE2B 626b8a3d11431582d7ff3eb24815e64b67394e2beff068b084f0dc4d6d7249548f42dc6ddbf0fbfab0ca7f7e2285f7fc80c588f9be3ecc68181fe1fe4a22d22a SHA512 2c2857d4f873e171454e49436636ee62fc639126bfb165f26615fbcab4988783a02a265a3b1e4b6257d276badd602e1a42f079374b360d25f7712057755ecd44
diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild
deleted file mode 100644
index a959252a0..000000000
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
-	https://github.com/Gaius-Augustus/Augustus"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-# LICENSE="GPL-3"
-# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
-# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="bam2wig examples man mysql sqlite"
-
-RDEPEND="
-	bam2wig? ( sci-biology/samtools:0.1-legacy )
-	sci-biology/bamtools
-	>=sci-mathematics/lpsolve-5.5
-	sci-libs/gsl
-	sci-libs/suitesparse
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( dev-db/mysql++ )
-	>=dev-libs/boost-1.49.0
-	sys-libs/zlib"
-DEPEND="${RDEPEND}
-	sys-devel/flex"
-S="${WORKDIR}/Augustus-${PV}"
-
-src_prepare() {
-	# TODO: do we need anything from the 2.5.5 patch?
-	# epatch "${FILESDIR}"/${P}-sane-build.patch
-	default
-	tc-export CC CXX
-	# lets respect upstream's wish and keep -ggdb
-	sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die
-	sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \
-		-i auxprogs/bam2wig/Makefile || die
-	sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" \
-		-i auxprogs/bam2wig/Makefile || die
-	# https://github.com/Gaius-Augustus/Augustus/issues/53
-	sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile || die
-	sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die
-	# enable comparative gene prediction (CGP, needs c++11 compiler),
-	#    this needs sci-mathematics/lpsolve
-	sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
-	# enable compressed gzip input
-	sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die
-	# comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite
-	#    supposedly pick only either a single-one
-	if use mysql; then
-		sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die
-	elif use sqlite; then
-		# comparative (mutli-species, CGP) AUGUSTUS with SQLite
-		sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die
-	fi
-	# respect $EPREFIX in all Makefile's
-	find . -name Makefile | while read f; do \
-		sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die;
-	done
-}
-
-src_compile() {
-	emake clean && default
-
-	# compile stuff not compiled by default
-	# https://github.com/Gaius-Augustus/Augustus/issues/52
-	cd auxprogs/aln2wig || die
-	emake
-}
-
-src_install() {
-	dobin bin/*
-
-	exeinto /usr/libexec/${PN}
-	doexe scripts/*.{pl,pm,py} scripts/checkUTR
-	insinto /usr/libexec/${PN}
-	doins scripts/*.conf
-
-	insinto /usr/share/${PN}
-	doins -r config
-
-	echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
-
-	insinto /usr/libexec/${PN}/gbrowse
-	doins scripts/gbrowse.conf
-	insinto /usr/libexec/${PN}/gfftools
-	doins scripts/gff2ps_mycustom # config setting
-
-	dodoc README.md README-cgp.txt HISTORY.TXT auxprogs/homGeneMapping/README.TXT
-	dodoc -r docs/*.{pdf,txt}
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r docs/tutorial examples
-	fi
-
-	use man && doman mansrc/*.1
-
-	# install stuff compiled but not written into bin/
-	# https://github.com/Gaius-Augustus/Augustus/issues/14
-	dobin auxprogs/utrrnaseq/Debug/utrrnaseq
-	dodoc auxprogs/utrrnaseq/doc/reference.pdf
-	# https://github.com/Gaius-Augustus/Augustus/issues/51
-	dobin auxprogs/checkTargetSortedness/checkTargetSortedness \
-		auxprogs/compileSpliceCands/compileSpliceCands
-
-	# ./augustus-training/ contains web application and setup
-}
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
deleted file mode 100644
index 6b4a3e5b5..000000000
--- a/sci-biology/augustus/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="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="man">install preformatted manual pages</flag>
-		<flag name="bam2wig">compile and install bam2wig conversion utility</flag>
-	</use>
-</pkgmetadata>