sci-biology/paml: Version bump to 4.9j

Bug: https://bugs.gentoo.org/706708
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>

1 files changed, 43 insertions, 0 deletions

diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild
new file mode 100644
index 000000000000..e8a5d07ee40c
--- /dev/null
+++ b/sci-biology/paml/paml-4.9j.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${P/-/}"
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.9j-makefile.patch
+	"${FILESDIR}"/${PN}-4.9j-fno-common.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.txt doc/.
+
+	insinto /usr/share/${PN}/control
+	doins *.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r stewart* *.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}