From 80a18f092e75c49d6cd4dae6a460c197988095b7 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri, 20 Mar 2015 23:21:41 +0100
Subject: sci-biology/angsd: new package, -9999 compiles fine, need a snapshot
 for 0.700 version or whichever

Package-Manager: portage-2.2.15
---
 sci-biology/angsd/ChangeLog         | 10 ++++++++
 sci-biology/angsd/angsd-9999.ebuild | 49 +++++++++++++++++++++++++++++++++++++
 sci-biology/angsd/metadata.xml      |  9 +++++++
 3 files changed, 68 insertions(+)
 create mode 100644 sci-biology/angsd/ChangeLog
 create mode 100644 sci-biology/angsd/angsd-9999.ebuild
 create mode 100644 sci-biology/angsd/metadata.xml

diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog
new file mode 100644
index 000000000..a0ed7633e
--- /dev/null
+++ b/sci-biology/angsd/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/angsd
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*angsd-9999 (20 Mar 2015)
+
+  20 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +angsd-9999.ebuild,
+  +metadata.xml:
+  sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700
+  version or whichever
diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild
new file mode 100644
index 000000000..2850ddc45
--- /dev/null
+++ b/sci-biology/angsd/angsd-9999.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit git-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Population genetics analysis package"
+HOMEPAGE="http://www.popgen.dk/angsd"
+if [ "$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
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+
+DEPEND="dev-lang/R
+	sci-libs/htslib"
+RDEPEND="${DEPEND}"
+
+# https://github.com/ANGSD/angsd/issues/9
+src_prepare(){
+	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@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(){
+	emake HTS=/usr/include
+}
+
+src_install(){
+	dobin angsd
+	dodoc README.md
+	cd misc || die
+	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
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/angsd/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
-- 
cgit v1.2.3-65-gdbad