sci-biology/pairagon: Fix double-prefix

Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702
Package-Manager: Portage-2.3.8, Repoman-2.3.3

1 files changed, 20 insertions, 17 deletions

diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index c23129f74..843198232 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-functions toolchain-funcs
 
 DESCRIPTION="HMM-based cDNA to genome aligner"
 HOMEPAGE="http://mblab.wustl.edu/software.html"
@@ -15,26 +14,30 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="dev-lang/perl"
+DEPEND="dev-lang/perl:="
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}"/pairagon
+S=${WORKDIR}/${PN}
 
-src_prepare(){
-	sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile
-	sed -e 's/^use Alignment/use pairagon::Alignment/' -i bin/alignmentConvert.pl || die
+src_prepare() {
+	default
+
+	sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' \
+		-i Makefile || die
+	sed -e 's/^use Alignment/use pairagon::Alignment/' \
+		-i bin/alignmentConvert.pl || die
 }
 
-src_compile(){
+src_compile() {
 	emake pairagon-linux
 }
 
-src_install(){
-	dobin bin/pairagon bin/pairameter_estimate bin/Pairagon.pl bin/alignmentConvert.pl
-	dodoc README
-	perl_set_version
+src_install() {
+	dobin bin/{pairagon,pairameter_estimate,Pairagon.pl,alignmentConvert.pl}
+	einstalldocs
+
 	insinto /usr/share/pairagon
-	doins parameters/*
-	insinto ${VENDOR_LIB}/${PN}
-	doins lib/perl5/Alignment.pm
+	doins -r parameters/.
+
+	perl_domodule -C ${PN} lib/perl5/Alignment.pm
 }