reinit the tree, so we can have metadata

9 files changed, 352 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
new file mode 100644
index 000000000000..a1c0d2db95c5
--- /dev/null
+++ b/sci-biology/vienna-rna/Manifest
@@ -0,0 +1,12 @@
+AUX vienna-rna-2.1.1-bindir.patch 361 SHA256 cf5f393cb9ad1aba9e054d9ba7a0f876812ee88f2fa4d619ddc0b0ae2de3136a SHA512 f2e9da29f1ae3c1d3e7594367ef13ad0d44ebbcf1d9badf9d55c415e50b7e5af170dba7bcdad6438505786b941518f84ddb154cf1a6df60a229f3856cf333a94 WHIRLPOOL 5d28000ea19a6fbec28ff2a893ae77bc4ba0a70d74b5cb510a37d09563f278789379ee72e4aabc4facda873f6992ef707bd14732407547372174a1a4b9cccefc
+AUX vienna-rna-2.1.1-impl-decl.patch 354 SHA256 9f9005092b060db501b51c37f215f9ca87da53720609ce971c3d9ad6bcf2ea39 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b WHIRLPOOL 02ce683c58e4f5715ab75445d9efeb02c1c104a6faa25b19739dc43931f813d6c7637a6690026d18607da98f2f7a7185ffe3491c237d1f40dd09340dc44c651e
+AUX vienna-rna-2.1.1-prll.patch 885 SHA256 0438173aa9d336ae41d7024d66dd6b07c1bac3c812750198ef0113e6a8407dee SHA512 1b80636b43e1ce9ca54431358b45f2503ef3f49b8cd049b5ef501058e1771bda3628c88e63cc1bea9a32aff5a004ccef663b47dae385a5df6071793f292dff94 WHIRLPOOL 6a0661741d7aa0f0461c7dbc68b2967e10f380cf8c42c699fe7ae568e48441bc0e726c2c49942af1f9f2557725de1545718fa66fa336de00f84ea1660b984898
+AUX vienna-rna-2.1.1-setup.py 810 SHA256 035f9c8aff6b6bc575b089e48e79bffe7da093de499a1d88eb1785346025940a SHA512 57feac6d5701a25fcda01f93f506a422d4639595a7d0ef73575af88f283fabc3730a8ea3e116ccfd417b015611c813f08ff047c9e362eaa74d2ce275ae65f8b8 WHIRLPOOL 8d9eb802bb055e30992a9509c43638e5602d434c5237729d816833f3e10f858ead48fb228728c5842a9e09b678f85091fab32b976ca8db4cc023c4fad2382b85
+AUX vienna-rna-2.1.8-bindir.patch 367 SHA256 44f43ad3cec8e05107c67f6f8420573a8f85ee80c4ac62abd6c7166192b6ecfc SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf WHIRLPOOL a74ee28add9902d2a4c3219fef94d85c96934d7b113b69b3a09faa8d104c0d83d50fcea953a3073a48958f5d6e94d075697b2ceade3b21b236a2882aab4843fa
+DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f
+DIST ViennaRNA-2.1.8.tar.gz 5464683 SHA256 37a0a0b7c8a167bcdab1a85d88bcb1025ad8e00a4b00a147bf36d45dc8ca7560 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e WHIRLPOOL a79f30d49c9bbe047d9fe83054dc08e94535f17417ef1f412bbcdd374d1988a8f2faf679e154c1ed1d1a75799e6cc0232d30b3adf65b3fa19978322f67ace57e
+EBUILD vienna-rna-2.1.1.ebuild 2667 SHA256 9f6008c2895d9b6588e3305ee324906ab7d0e04f92947c59710335b0e7b29d56 SHA512 22b96fce6750fd8094e6943abd8085ec5e3035f66766f56a6a840f591faaebbffece2b0174e7db078d4e96bae30762bc6d15e21bc2e45a6e086115ddb2ca4bc1 WHIRLPOOL 18416ab6427db4f63a89c64c50bf2f8c4c78a4bf266907006707e3b045d240115c3777dce226e305b13dab895333851fb716c580701baa02777c28c1ed5772c5
+EBUILD vienna-rna-2.1.8.ebuild 2588 SHA256 9e2ef28f2b8020524fa9b29b07b4988a8977d961ceaa397979ffd8adc02045c8 SHA512 4474f2bf042a31e02fd7b9882f6b5ec17fef4ba9f23eab29a39e9c09ea29414e836c029e568a905a2c315370c763384f9d84547a56a8806216dc825d51c3d378 WHIRLPOOL 0adeaaf4815be6b2c2f2b3f6a1b5e5ce6e67abe2cc38e48f49e2308670d5d6793e0358d5aa16a3443b283bea7041f78a2f40cb7e775e28c885b82529a97bd9c4
+MISC ChangeLog 3325 SHA256 5216a998d8538cee5696af5084bfa0aa5f77b3a094e83d7ccae8e46ec7f7bf8c SHA512 77246295b10a7d717b4a335f837fc2ec28468eb2dd996d6c1efb724a11e32f47c905a4216cf2f00a0333f5c760eddbb463ed5710d3f5b92cb3d7c6e3d782356b WHIRLPOOL 295dc20d4686d5e6297ad203d4222423f222de9cc0d101296ed26b122ca8728ed2787503a91f85424608eb8fcc28aed1c3313e42da93bebdd5610b5608f8f87c
+MISC ChangeLog-2015 8565 SHA256 523813579b1e0c6beebf4e9aba734bc303dd41d88d0c57b936349cd3e4c185aa SHA512 b9f29ac13ca0774fbf2ea981876b04d07f2c7f8b5b601a507a64c90d1fea5c7b43eeb18a210588524f19e950437b7d3410ceecd877b9373ef7ab83e575a8b8ee WHIRLPOOL 83f012a519a5c50a310fcae41ffcb4a86db6b9212527b44a6d85c062adce90281820ce07caf2c8ae8a42248ece67f5fc791065dae9355c8952afe2a98d7ac196
+MISC metadata.xml 1315 SHA256 5afca47f48661e11afe2649369997eef235bb1224c0632912a3f43bcd37b53f5 SHA512 5aa9cb8fb220b9d6b0ca7c0a32a26eae6eb5e8585eb73a6668ef28821196617247c8dbe0dba5f10b76d0d5a3a86b1430e3d4616ff084fcd09fa108481e08068e WHIRLPOOL 3345b4e2f80c72ac38bb93cc4d12802dfcc2a0445847bf5b4e0858740aec95fdd13247796a85392ccb3fd47e4b5740b0b28233ae3d508435bfb14f3082583736
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
new file mode 100644
index 000000000000..6d35ecea9b0f
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-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
+ 
+ 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/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
new file mode 100644
index 000000000000..de457f318e8e
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
@@ -0,0 +1,15 @@
+ Readseq/readseq.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/Readseq/readseq.c b/Readseq/readseq.c
+index 8af7b39..56a25ae 100644
+--- a/Readseq/readseq.c
++++ b/Readseq/readseq.c
+@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
new file mode 100644
index 000000000000..ee4aef5c3308
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
@@ -0,0 +1,30 @@
+ Readseq/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Readseq/Makefile b/Readseq/Makefile
+index f073aaa..05f2edd 100644
+--- a/Readseq/Makefile
++++ b/Readseq/Makefile
+@@ -6,11 +6,11 @@
+ #
+ 
+ # pick an ANSI C compiler (the default Sun CC is not ANSI)
+-CC=gcc  # Gnu C Compiler
++CC?=gcc  # Gnu C Compiler
+ #CC=cc  # SGI Irix
+ #CC=vcc # some DEC Ultrix
+ 
+-CFLAGS=
++CFLAGS?=
+ #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
+ #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+ 
+@@ -40,7 +40,7 @@ all: build test
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
new file mode 100644
index 000000000000..57f6b712ba3d
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
@@ -0,0 +1,27 @@
+from distutils.core import setup, Extension
+import os
+import sys
+ 
+old_filename = os.path.join("Perl", "RNA.py")
+new_filename = os.path.join("Perl", "__init__.py")
+if os.path.exists(old_filename):
+    os.rename(old_filename, new_filename)
+ 
+extra_link_args = []
+ 
+extension = Extension("_RNA",
+                      ["Perl/RNA_wrap.c"],
+                      libraries=['RNA'],
+                      library_dirs=['lib'],
+                      extra_link_args=extra_link_args
+                      )
+ 
+setup(name="RNA",
+      version="2.1.1",
+      description="Vienna RNA",
+      author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
+      url="http://www.tbi.univie.ac.at/RNA/",
+      package_dir = {'RNA':'Perl'},
+      packages = ['RNA'],
+      ext_modules=[extension],
+      )
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/metadata.xml b/sci-biology/vienna-rna/metadata.xml
new file mode 100644
index 000000000000..861e9e38c31c
--- /dev/null
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription>
+	The Vienna RNA Package consists of a C code library and several
+	stand-alone programs for the prediction and comparison of RNA secondary
+	structures. RNA secondary structure prediction through energy
+	minimization is the most used function in the package. We provide three
+	kinds of dynamic programming algorithms for structure prediction: the
+	minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
+	single optimal structure, the partition function algorithm of
+	(McCaskill 1990) which calculates base pair probabilities in the
+	thermodynamic ensemble, and the suboptimal folding algorithm of
+	(Wuchty et.al 1999) which generates all suboptimal structures within a
+	given energy range of the optimal energy. For secondary structure
+	comparison, the package contains several measures of distance
+	(dissimilarities) using either string alignment or tree-editing
+	(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
+	sequences with a predefined structure (inverse folding).
+</longdescription>
+</pkgmetadata>
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..8b760b5a84bf
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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} )"
+
+RDEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+	python? ( dev-lang/swig:0 )"
+
+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
+}
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..7664f6d3dc6e
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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} )"
+
+RDEPEND="
+	dev-lang/perl
+	media-libs/gd
+	doc? ( dev-texlive/texlive-latex )
+	python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+	python? ( dev-lang/swig:0 )"
+
+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)
+	perl_delete_localpod || die "Failed to remove perlocal.pod"
+	if use python; then
+		cd interfaces/Python || die
+		distutils-r1_src_install
+	fi
+}