From 10febb5681bdc497d34f2c58667e31124437fa65 Mon Sep 17 00:00:00 2001
From: Justin Lecher <jlec@gentoo.org>
Date: Sun, 14 Feb 2016 18:32:26 +0100
Subject: sci-biology/angsd: Bump to EAPI=6

* Use git-r3.eclass

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec@gentoo.org>
---
 sci-biology/angsd/angsd-9999.ebuild | 41 +++++++++++++++++++------------------
 sci-biology/angsd/metadata.xml      |  2 +-
 2 files changed, 22 insertions(+), 21 deletions(-)

(limited to 'sci-biology/angsd')

diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
index e4c2be65a..0de57d45d 100644
--- a/sci-biology/angsd/angsd-9999.ebuild
+++ b/sci-biology/angsd/angsd-9999.ebuild
@@ -1,40 +1,39 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
-inherit git-2
-
-[ "$PV" == "9999" ] && inherit git-2
+inherit git-r3
 
 DESCRIPTION="Population genetics analysis package"
 HOMEPAGE="http://www.popgen.dk/angsd"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
-	KEYWORDS=""
-else
-	EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
-	EGIT_BRANCH="0.700"
-	KEYWORDS=""
-fi
+EGIT_REPO_URI="https://github.com/ANGSD/angsd.git"
 
 LICENSE="GPL-2"
 SLOT="0"
+KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-lang/R
+DEPEND="
+	dev-lang/R
 	sci-libs/htslib"
 RDEPEND="${DEPEND}"
 
 # https://github.com/ANGSD/angsd/issues/9
 src_prepare(){
-	sed -e 's@FLAGS=-O3@FLAGS=@' \
+	sed \
+		-e 's@FLAGS=-O3@FLAGS=@' \
+		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
+		-e 's@all: htshook angsd misc@all: angsd misc@' \
+		-i Makefile || die
+	sed \
 		-e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-		-e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die
-	sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \
-		-e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die
-	sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die
+		-e 's@HTSDIR = .*@HTSDIR = /usr/include@' \
+		-i misc/Makefile || die
+	sed \
+		-e 's@include "../htslib/bgzf.h@include "bgzf.h@' \
+		-i misc/thetaStat.cpp || die
 }
 
 src_compile(){
@@ -45,5 +44,7 @@ src_install(){
 	dobin angsd
 	dodoc README.md
 	cd misc || die
-	dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix
+	dobin \
+		supersim thetaStat realSFS emOptim2 msToGlf smartCount \
+		printIcounts splitgl contamination NGSadmix
 }
diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml
index 1699e58b2..f68a1b6fa 100644
--- a/sci-biology/angsd/metadata.xml
+++ b/sci-biology/angsd/metadata.xml
@@ -5,7 +5,7 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
-<maintainer type="project">
+  <maintainer type="project">
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
-- 
cgit v1.2.3-65-gdbad