proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

1 files changed, 113 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
new file mode 100644
index 000000000000..df5c8eb50f90
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_OPTIONAL=true
+AUTOTOOLS_AUTORECONF=true
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="vienna-rna"
+KEYWORDS="amd64 ppc x86"
+IUSE="doc openmp python static-libs"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? (
+		${PYTHON_DEPS}
+		dev-lang/swig )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-bindir.patch
+	"${FILESDIR}"/${P}-prll.patch
+	"${FILESDIR}"/${P}-impl-decl.patch
+)
+
+src_prepare() {
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
+
+	autotools-utils_src_prepare
+
+	if use python; then
+		cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
+		PATCHES=()
+		distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local myeconfargs=(
+		--with-cluster
+		$(use_enable openmp) )
+
+	use doc || \
+		myeconfargs+=(
+			--without-doc-pdf
+			--without-doc-html
+			--without-doc
+			)
+	autotools-utils_src_configure
+	sed \
+		-e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i RNAforester/g2-0.70/Makefile || die
+	sed \
+		-e "s:CC=gcc:CC=$(tc-getCC):" \
+		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die
+	use python && distutils-r1_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+	# TODO: Add (optional?) support for the NCBI toolkit.
+	if use python; then
+		pushd Perl > /dev/null
+			mv RNA_wrap.c{,-perl} || die
+			swig -python RNA.i || die
+		popd > /dev/null
+		distutils-r1_src_compile
+		mv Perl/RNA_wrap.c{-perl,} || die
+	fi
+}
+
+src_test() {
+	autotools-utils_src_compile -C Perl check
+	autotools-utils_src_compile -C Readseq test
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	if ! use static-libs; then
+		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
+	fi
+
+	newbin Readseq/readseq readseq-vienna
+	dodoc Readseq/Readseq.help
+	newdoc Readseq/Readme README.readseq
+	newdoc Readseq/Formats Formats.readseq
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	perl_delete_localpod || die "Failed to remove perlocal.pod"
+	use python && distutils-r1_src_install
+}