[gentoo-commits] proj/sci:master commit in: sci-biology/velvet/

[Justin Lecher]

commit:     48c8d6e83f00a3d7eb17c077fa4c13ab1f5c1ab6
Author:     mahnmut <mahnmut411 <AT> gmail <DOT> com>
AuthorDate: Thu Dec 26 17:29:46 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 26 17:29:46 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=48c8d6e8

Create velvet-1.2.1O.ebuild

---
 sci-biology/velvet/velvet-1.2.1O.ebuild | 54 +++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/sci-biology/velvet/velvet-1.2.1O.ebuild b/sci-biology/velvet/velvet-1.2.1O.ebuild
new file mode 100644
index 0000000..9e0dd6e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.1O.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.1O.ebuild,v 1.5 2013/09/19 09:02:55 mahn Exp $
+# adapt from phajdan.jr ebuild
+
+EAPI=4
+
+inherit eutils toolchain-funcs flag-o-matic
+
+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/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="-doc"
+KEYWORDS="amd64 x86"
+
+RDEPEND="sys-libs/zlib"
+DEPEND="${RDEPEND}
+        doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+        # necessary?
+        append-flags -O3 # as recommended by upstream
+        use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+}
+
+src_compile() {
+        tc-export CC
+        MAKE_XOPTS=""
+        if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
+        if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
+        emake -j1 $MAKE_XOPTS || die
+        emake -j1 $MAKE_XOPTS color || die
+}
+
+src_install() {
+        dobin velvet{g,h,g_de,h_de} || die
+        insinto /usr/share/${PN}
+        doins -r contrib || die
+        dodoc Manual.pdf CREDITS.txt ChangeLog || die
+}
+
+pkg_postinst() {
+        elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+        elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+        elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+        elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+}