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

[Justin Lecher]

commit:     38b3a2d1841263f329ff7e682df93c6af78ecf07
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:20:09 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:20:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38b3a2d1

merged into tree

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-biology/velvet/ChangeLog            | 11 -----
 sci-biology/velvet/metadata.xml         |  5 ---
 sci-biology/velvet/velvet-1.2.10.ebuild | 73 ---------------------------------
 3 files changed, 89 deletions(-)

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
deleted file mode 100644
index 9efc41e..0000000
--- a/sci-biology/velvet/ChangeLog
+++ /dev/null
@@ -1,11 +0,0 @@
-# ChangeLog for sci-biology/velvet
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*velvet-1.2.10 (28 Dec 2013)
-
-  28 Dec 2013; Justin Lecher <jlec@g.o> -velvet-1.2.1O.ebuild,
-  +velvet-1.2.10.ebuild, +metadata.xml:
-  Some improvements regarding die and optional enviromental variables; respect
-  CC, CFLAGS
-

diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/velvet/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-</pkgmetadata>

diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
deleted file mode 100644
index 3ed797e..0000000
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2013 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 $
-
-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 recommendes using -O3 in CFLAGS"
-	echo
-	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"
-	MAKEOPTS+=" -j1"
-
-	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}"
-	)
-	if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
-	if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
-}
-
-src_compile() {
-	emake "${MAKE_XOPTS[@]}"
-	emake "${MAKE_XOPTS[@]}" color
-}
-
-src_test() {
-	emake "${MAKE_XOPTS[@]}" test
-}
-
-src_install() {
-	dobin velvet{g,h,g_de,h_de}
-	insinto /usr/share/${PN}
-	doins -r contrib
-	dodoc Manual.pdf CREDITS.txt ChangeLog
-}