reinit the tree, so we can have metadata

1 files changed, 76 insertions, 0 deletions

diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
new file mode 100644
index 000000000000..d5a93f2f3e48
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+	if ! use doc; then
+		sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+	fi
+	elog "Upstream recommends using -O3 in CFLAGS"
+	echo
+	elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
+	elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
+	elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
+	elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
+	elog "the package. For example:"
+	elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+
+	if [[ $(tc-getCC) =~ gcc ]]; then
+		local eopenmp=-fopenmp
+	elif [[ $(tc-getCC) =~ icc ]]; then
+		local eopenmp=-openmp
+	else
+		elog "Cannot detect compiler type so not setting openmp support"
+	fi
+	append-flags -fPIC ${eopenmp}
+	append-ldflags ${eopenmp}
+
+	tc-export CC
+
+	MAKE_XOPTS=(
+		CC=$(tc-getCC)
+		CFLAGS="${CFLAGS}"
+		OPT="${CFLAGS}"
+	)
+	use openmp && MAKE_XOPTS+=( OPENMP=1 )
+	[[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} )
+	[[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} )
+	[[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
+	[[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} )
+}
+
+src_compile() {
+	emake "${MAKE_XOPTS[@]}" -j1
+	emake "${MAKE_XOPTS[@]}" -j1 color
+}
+
+src_test() {
+	emake "${MAKE_XOPTS[@]}" -j1 test
+}
+
+src_install() {
+	dobin velvet{g,h,g_de,h_de}
+	insinto /usr/share/${PN}
+	doins -r contrib
+	dodoc Manual.pdf CREDITS.txt ChangeLog
+}