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, 93 insertions, 0 deletions

diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
new file mode 100644
index 000000000000..5a988dfac24d
--- /dev/null
+++ b/sci-biology/poa/Manifest
@@ -0,0 +1 @@
+DIST poaV2.tar.gz 62612 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2
diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch
new file mode 100644
index 000000000000..bdd638cf64b7
--- /dev/null
+++ b/sci-biology/poa/files/2-respect-flags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index a65bed0..713a7ab 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,9 +26,10 @@ LIBOBJECTS= \
+ 	stringptr.o
+ 
+ 
+-CC = gcc
++CC ?= gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+ 
+@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS)
+ 
+ # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
+ poa: $(OBJECTS) liblpo.a
+-	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
+ 
+ what:
+ 	@echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch
new file mode 100644
index 000000000000..2ae08db4ff4d
--- /dev/null
+++ b/sci-biology/poa/files/respect-cflags.patch
@@ -0,0 +1,13 @@
+diff -urN poaV2.orig/Makefile poaV2/Makefile
+--- poaV2.orig/Makefile	2004-03-11 21:33:30.000000000 -0800
++++ poaV2/Makefile	2006-03-09 20:09:27.000000000 -0800
+@@ -28,7 +28,8 @@
+ 
+ CC = gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+ 
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
new file mode 100644
index 000000000000..65027f64ec24
--- /dev/null
+++ b/sci-biology/poa/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="sourceforge">poamsa</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
new file mode 100644
index 000000000000..8a1a23ca4902
--- /dev/null
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+MY_P="${PN}V${PV}"
+
+DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
+HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
+SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+
+# According to SF project page
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="static-libs"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-respect-flags.patch
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		OPT_CFLAGS="${CFLAGS}" \
+		poa
+}
+
+src_install() {
+	dobin "${S}"/poa "${S}"/make_pscores.pl
+	use static-libs && dolib.a "${S}"/liblpo.a
+	dodoc "${S}"/README "${S}"/multidom.*
+	insinto /usr/share/poa
+	doins "${S}"/*.mat
+}
+
+pkg_postinst() {
+	elog "poa requires a score matrix as the first argument."
+	elog "This package installs two examples to ${EROOT}usr/share/poa/."
+}