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

5 files changed, 107 insertions, 0 deletions

diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
new file mode 100644
index 000000000000..7e64fe420af6
--- /dev/null
+++ b/sci-biology/raxml/Manifest
@@ -0,0 +1 @@
+DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 WHIRLPOOL 7fe7ac66412c979d3ecca17e2c06a32566fefe7bdcf39664a0885fcdebc2b8187c222ca5e29cf2685085fba21a8aff0a2aefceec08823cab155a5f62f8b59490
diff --git a/sci-biology/raxml/files/raxml-7.2.5-makefile.patch b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
new file mode 100644
index 000000000000..8b381e50cb58
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 8d09549..59af556 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 
++CFLAGS += -D_GNU_SOURCE
+ #-Wall -std=c99 -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport -pedantic-errors -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
new file mode 100644
index 000000000000..ae83e2eef4e7
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 716b6c6..f0c1de2 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse
++CFLAGS += -D_GNU_SOURCE
+ 
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/raxml/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/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
new file mode 100644
index 000000000000..b9ace2a0ec0f
--- /dev/null
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
+HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
+SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse3 +threads"
+
+REQUIRED_USE="cpu_flags_x86_sse3"
+
+# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
+DEPEND="" # mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/RAxML-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-makefile.patch
+
+	use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3
+	use threads && \
+		append-cflags -D_USE_PTHREADS && \
+		append-ldflags -pthread
+
+	tc-export CC
+}
+
+src_compile() {
+	emake -f Makefile.gcc
+}
+
+src_install() {
+	dobin raxmlHPC
+}