sci-biology/augustus: add version 3.4.0

Closes: https://bugs.gentoo.org/515996
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

sci-biology/augustus/Manifest

@@ -1 +1,2 @@
+DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6
 DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f

sci-biology/augustus/augustus-3.4.0.ebuild

@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DOCS_BUILDER="doxygen"
+DOCS_CONFIG_NAME="doxygen.conf"
+inherit docs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${P^}"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-db/sqlite:3
+	dev-db/mysql++
+	dev-db/mysql-connector-c
+	dev-libs/boost:=
+	sci-biology/bamtools
+	sci-libs/gsl
+	sci-libs/htslib
+	sci-libs/suitesparse
+	sci-mathematics/lpsolve
+	sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+	default
+	docs_compile
+}
+
+src_install() {
+	einstalldocs
+	# from upstream Makefile install:
+	dodir "opt/${P}"
+	cp -a config bin scripts "${ED}/opt/${P}" || die
+	local file
+	for file in bin/*; do
+		dosym "../${P}/${file}" "/opt/${file}"
+	done
+}