sci-biology/augustus: version bump, fix awful Makefile's

Do not require static libraries. Only bamtools are really needed.
htslib is not needed. For bam2wig samtools-0.2 series is needed.

I decided to blindly install some of the binaries created but not
copied into `./bin/`.

`src/Makefile` will gladly define mysql and sqlite together, probably
a non-sense. We force mysql as we check for it first. Not sure if
sqlite should be preferred.

I documented in the augustus-3.3.2.ebuild other "forgotten" files,
like gbrowse.conf and a template for gff2ps.

I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`.

Gaius-Augustus/Augustus#14
Gaius-Augustus/Augustus#50
Gaius-Augustus/Augustus#51
Gaius-Augustus/Augustus#52
Gaius-Augustus/Augustus#53

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

sci-biology/augustus/Manifest

@@ -1 +1 @@
-DIST augustus-3.3.tar.gz 125296783 BLAKE2B 37479eb1eb8cf702438e4c0da659bf43133fb8268960c3e4f0357c105b740447d903a198cb9de06cbbc4d237dd03daefd662afdc35615edefe5f36ddc832ed2c SHA512 c6acfc5cb358cac60b68da7e726a871ad898654e154ccb83d86f1a13aa45643b0e63f2af1017a8ab12616677818709abefb1df4b40b6f7b971c18dbc7519837f
+DIST augustus-3.3.2.tar.gz 235794642 BLAKE2B 626b8a3d11431582d7ff3eb24815e64b67394e2beff068b084f0dc4d6d7249548f42dc6ddbf0fbfab0ca7f7e2285f7fc80c588f9be3ecc68181fe1fe4a22d22a SHA512 2c2857d4f873e171454e49436636ee62fc639126bfb165f26615fbcab4988783a02a265a3b1e4b6257d276badd602e1a42f079374b360d25f7712057755ecd44

sci-biology/augustus/augustus-3.3.2.ebuild

@@ -0,0 +1,115 @@
+# 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/3.3.2.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 not 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
+}

sci-biology/augustus/metadata.xml

@@ -5,4 +5,8 @@
 		<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>