merged into tree

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

4 files changed, 0 insertions, 90 deletions

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
deleted file mode 100644
index 9efc41ec2..000000000
--- 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@gentoo.org> -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/Manifest b/sci-biology/velvet/Manifest
deleted file mode 100644
index 4d3396411..000000000
--- a/sci-biology/velvet/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
deleted file mode 100644
index f17a827e3..000000000
--- 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 3ed797e89..000000000
--- 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
-}