From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001
From: "Robin H. Johnson" <robbat2@gentoo.org>
Date: Sat, 8 Aug 2015 13:49:04 -0700
Subject: proj/gentoo: Initial commit
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This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
---
 sci-biology/emboss/emboss-6.6.0.ebuild | 61 ++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 sci-biology/emboss/emboss-6.6.0.ebuild

(limited to 'sci-biology/emboss/emboss-6.6.0.ebuild')

diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
new file mode 100644
index 00000000000..22d650f1107
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+inherit autotools-utils emboss-r1 eutils readme.gentoo
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE+=" minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
+
+RDEPEND+=" !sys-devel/cons"
+PDEPEND+="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/primer3
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		)"
+
+S="${WORKDIR}"/EMBOSS-${PV}
+
+DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )
+
+PATCHES=(
+	"${FILESDIR}"/${P}_fix-build-system.patch
+	"${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+	"${FILESDIR}"/${P}_plplot-declarations.patch
+	"${FILESDIR}"/${P}_qa-implicit-declarations.patch
+)
+
+src_install() {
+	# Use autotools-utils_* to remove useless *.la files
+	autotools-utils_src_install
+
+	readme.gentoo_create_doc
+
+	# Install env file for setting libplplot and acd files path.
+	cat > 22emboss <<- EOF
+		# ACD files location
+		EMBOSS_ACDROOT="${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."
+}
-- 
cgit v1.2.3-18-g5258