sci-biology/grass: introduce -9999 live version, drop old

fix the build system (https://github.com/AlexeyG/GRASS/issues/6)

Package-Manager: portage-2.3.2

1 files changed, 42 insertions, 0 deletions

diff --git a/sci-biology/grass/grass-9999.ebuild b/sci-biology/grass/grass-9999.ebuild
new file mode 100644
index 000000000..2f592d28c
--- /dev/null
+++ b/sci-biology/grass/grass-9999.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit git-r3 eutils
+
+DESCRIPTION="Scaffold next-generation sequencing assemblies"
+HOMEPAGE="https://github.com/AlexeyG/GRASS"
+#SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip
+#	https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf"
+EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# some IBM development CPLEX library?
+# ilcplex/ilocplex.h: No such file or directory
+# https://github.com/AlexeyG/GRASS/issues/6
+DEPEND="sci-biology/bamtools
+	sci-biology/ncbi-tools++
+	sys-cluster/openmpi"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	epatch "${FILESDIR}"/fix_Makefile_variablenames.patch
+#	sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die
+#	sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die
+#	sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die
+}
+
+src_compile(){
+	emake all
+}
+
+src_install(){
+	newdoc manual/manual.pdf grass_manual.pdf
+	dobin bin/*
+}