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

4 files changed, 71 insertions, 0 deletions

diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
new file mode 100644
index 000000000000..b1f7bb630cd0
--- /dev/null
+++ b/sci-biology/clustalw-mpi/Manifest
@@ -0,0 +1 @@
+DIST clustalw-mpi-0.13.tar.gz 154911 RMD160 9da3e418efcb0cfd0c5df2705ee217b9dacc3917 SHA1 ae5026e8b4ba58bb0caa5643ea90434d9589df5a SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
new file mode 100644
index 000000000000..11f1e57e2731
--- /dev/null
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm"
+HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"
+SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="public-domain"
+IUSE="mpi_njtree static_pairalign"
+
+DEPEND="virtual/mpi"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	if use mpi_njtree; then
+		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
+			die "Failed to configure MPI code for NJ trees."
+	fi
+	if use static_pairalign; then
+		sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
+			die "Failed to configure static scheduling for pair alignments."
+	fi
+}
+
+src_install() {
+	dobin ${PN}
+	newdoc README.${PN} README
+}
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
new file mode 100644
index 000000000000..6e36061cbb39
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
@@ -0,0 +1,23 @@
+ Makefile |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index f2107ce..835232b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE
+ PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
+ #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+ 
+-CFLAGS  = -c -O3
++CFLAGS  += -c
+ #CFLAGS  = -c -O3 -funroll-all-loops
+-LFLAGS	= -lm 
++LIBS	= -lm 
+ 
+ clustalw-mpi: $(OBJECTS) 
+-	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+ 
+ interface.o : interface.c $(HEADERS) param.h
+ 	$(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
new file mode 100644
index 000000000000..905eba1a07b8
--- /dev/null
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<use>
+  <flag name='mpi_njtree'>Use MPI (as opposed to serial) code for computing
+    neighbor-joining trees</flag>
+  <flag name='static_pairalign'>Use static (as opposed to dynamic) scheduling
+    for pair alignments</flag>
+</use>
+</pkgmetadata>