sci-biology/vienna-rna: Version Bump, #522850

Package-Manager: portage-2.2.12/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 152 insertions, 9 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 92d4c0ad8d00..2c9bb047caf6 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.53 2014/08/29 16:54:27 zlogene Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.54 2014/09/15 19:59:23 jlec Exp $
+
+*vienna-rna-2.1.8 (15 Sep 2014)
+
+  15 Sep 2014; Justin Lecher <jlec@gentoo.org> +vienna-rna-2.1.8.ebuild,
+  +files/vienna-rna-2.1.8-bindir.patch:
+  Version Bump, #522850
 
   29 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> -vienna-rna-1.8.5.ebuild,
   vienna-rna-2.1.1.ebuild:
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index 73129560d7a0..9547308e4d91 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,5 +1,5 @@
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 AUX vienna-rna-1.7.2-LDFLAGS.patch 978 SHA256 0c7db17c7a1a8a075e26f6b98b19c84a3f98f9ecdaa06755e4e426fcb1b8ce8c SHA512 a5fea1fc9c969d2bde9094b8303ee5d0b77f0570107d403279bcc3884d2925f81789d3d08627caadf92f435bbf369721dbc95e1122bde5741340104526a532b2 WHIRLPOOL 82d3e59c9a399cd352f72477fc9803012ef288e3198b0c69e86ce184cfe75c1c824b149b6ea55771da88180d9d402e1d8ed8444aac1f1bcd9211ded54f15d917
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 DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f
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diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
new file mode 100644
index 000000000000..e54dff95b485
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
@@ -0,0 +1,10 @@
+diff --git a/Utils/Makefile.am b/Utils/Makefile.am
+index f42ebf4..d84a0f1 100644
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -1,4 +1,4 @@
+-pkgbindir = $(pkgdatadir)/bin
++pkgbindir = $(prefix)/bin
+ pkgbin_PROGRAMS = b2ct popt ct2db
+ 
+ pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
new file mode 100644
index 000000000000..23691ee1623c
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild,v 1.1 2014/09/15 19:59:23 jlec Exp $
+
+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/RNA/packages/source/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
+	"${FILESDIR}"/${PN}-2.1.1-prll.patch
+	"${FILESDIR}"/${PN}-2.1.1-impl-decl.patch
+)
+
+src_prepare() {
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die
+
+	autotools-utils_src_prepare
+
+	if use python; then
+		cd interfaces/Python || die
+		local PATCHES=()
+		distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local myeconfargs=(
+		--with-cluster
+		$(use_enable openmp)
+	)
+
+	use doc || \
+		myeconfargs+=(
+			--without-doc-pdf
+			--without-doc-html
+			--without-doc
+			)
+	autotools-utils_src_configure
+	sed \
+		-e "s:CC=gcc:CC=$(tc-getCC):" \
+		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die
+	if use python; then
+		cd interfaces/Python || die
+		distutils-r1_src_configure
+	fi
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
+
+	# TODO: Add (optional?) support for the NCBI toolkit.
+	if use python; then
+		cd interfaces/Python || die
+		emake RNA_wrap.c
+		distutils-r1_src_compile
+	fi
+}
+
+src_test() {
+	autotools-utils_src_compile -C interfaces/Perl check
+	use python && autotools-utils_src_compile -C interfaces/Python 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)
+	fixlocalpod || die "Failed to remove perlocal.pod"
+	if use python; then
+		cd interfaces/Python || die
+		distutils-r1_src_install
+	fi
+}