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

[Justin Lecher]

commit:     900f13fe813b59aba02b9b8dbc5683a8634cfffc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:15:51 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:15:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=900f13fe

sci-biology/velvet: Some improvements regarding die and optional enviromental variables; respect CC, CFLAGS

Package-Manager: portage-2.2.7

---
 sci-biology/velvet/ChangeLog            | 11 +++++
 sci-biology/velvet/metadata.xml         |  5 +++
 sci-biology/velvet/velvet-1.2.10.ebuild | 73 +++++++++++++++++++++++++++++++++
 sci-biology/velvet/velvet-1.2.1O.ebuild | 54 ------------------------
 4 files changed, 89 insertions(+), 54 deletions(-)

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
new file mode 100644
index 0000000..9efc41e
--- /dev/null
+++ b/sci-biology/velvet/ChangeLog
@@ -0,0 +1,11 @@
+# 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
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/velvet/metadata.xml
@@ -0,0 +1,5 @@
+<?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
new file mode 100644
index 0000000..3ed797e
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,73 @@
+# 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
+}

diff --git a/sci-biology/velvet/velvet-1.2.1O.ebuild b/sci-biology/velvet/velvet-1.2.1O.ebuild
deleted file mode 100644
index 9e0dd6e..0000000
--- a/sci-biology/velvet/velvet-1.2.1O.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# 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"
-}