From 80392a26afc1e58165ac311b55d54d64ef2fa553 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sun, 19 Feb 2017 19:41:33 +0100
Subject: sci-biology/emboss: Port to emboss-r2.eclass

Package-Manager: portage-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3937
---
 sci-biology/emboss/emboss-6.6.0-r1.ebuild | 65 +++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 sci-biology/emboss/emboss-6.6.0-r1.ebuild

(limited to 'sci-biology/emboss')

diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
new file mode 100644
index 000000000000..6dc9b8566c7e
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2 readme.gentoo-r1
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
+
+RDEPEND="
+	!games-action/xbomber
+	!sys-devel/cons"
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/primer3
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+	)"
+
+S="${WORKDIR}/${P^^}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}_fix-build-system.patch
+	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+	"${FILESDIR}"/${P}_plplot-declarations.patch
+	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
+)
+
+src_install() {
+	emboss-r2_src_install
+
+	readme.gentoo_create_doc
+
+	# Install env file for setting libplplot and acd files path.
+	cat > 22emboss <<- EOF || die
+		# ACD files location
+		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
+	EOF
+	doenvd 22emboss
+
+	# Remove useless dummy files
+	find "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files"
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.gentoo".
+	mv "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \
+		|| die "Failed to move CODON directory"
+}
+
+pkg_postinst() {
+	readme.gentoo_print_elog
+}
-- 
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