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

6 files changed, 135 insertions, 0 deletions

diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest
new file mode 100644
index 000000000000..96826545f7c3
--- /dev/null
+++ b/sci-biology/prank/Manifest
@@ -0,0 +1,3 @@
+DIST prank.source.140603.tgz 150346 SHA256 9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 WHIRLPOOL 5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6
+DIST prank.src.100701.tgz 115444 SHA256 2ba63fc8f998a86e6fc688170b03f831eeb8d8deda95cbf0986e8a3a3b09ec79
+DIST prank.src.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c WHIRLPOOL 37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b
diff --git a/sci-biology/prank/files/prank-111130-gcc-4.7.patch b/sci-biology/prank/files/prank-111130-gcc-4.7.patch
new file mode 100644
index 000000000000..d7defbcadfec
--- /dev/null
+++ b/sci-biology/prank/files/prank-111130-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/check_version.cpp |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/check_version.cpp b/src/check_version.cpp
+index e968a05..6dfa062 100644
+--- a/src/check_version.cpp
++++ b/src/check_version.cpp
+@@ -8,6 +8,7 @@
+ #include <string>
+ #include <sstream>
+ #include <iostream>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml
new file mode 100644
index 000000000000..2cd3c04eeca0
--- /dev/null
+++ b/sci-biology/prank/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="google-code">prank-msa</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/prank/prank-100701.ebuild b/sci-biology/prank/prank-100701.ebuild
new file mode 100644
index 000000000000..913ff56ee71b
--- /dev/null
+++ b/sci-biology/prank/prank-100701.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S=${WORKDIR}/${PN}
+
+src_prepare() {
+	sed -i -e "s/\$(LINK)/& \$(LDFLAGS)/" Makefile || die
+}
+
+src_compile() {
+	emake \
+		LINK="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin prank
+}
diff --git a/sci-biology/prank/prank-111130.ebuild b/sci-biology/prank/prank-111130.ebuild
new file mode 100644
index 000000000000..4d4f6e912495
--- /dev/null
+++ b/sci-biology/prank/prank-111130.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://prank-msa.googlecode.com/files/prank.src.${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/prank-msa/src"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-4.7.patch
+	sed \
+		-e "s/\$(LINK)/& \$(LDFLAGS)/" \
+		-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
+		-i Makefile || die
+}
+
+src_compile() {
+	emake \
+		LINK="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin prank
+}
diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild
new file mode 100644
index 000000000000..a18b7ab9d553
--- /dev/null
+++ b/sci-biology/prank/prank-140603.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${PN}-msa/src"
+
+src_prepare() {
+	sed \
+		-e "s/\$(LINK)/& \$(LDFLAGS)/" \
+		-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
+		-i Makefile || die
+}
+
+src_compile() {
+	emake \
+		LINK="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+	dobin ${PN}
+}