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, 54 insertions, 0 deletions

diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest
new file mode 100644
index 000000000000..a63f193ecb5b
--- /dev/null
+++ b/sci-biology/piler/Manifest
@@ -0,0 +1 @@
+DIST piler-1.0.tar.gz 35220 SHA256 2940530c0afd7e49ca6e9cd8a1e3fd9890d87c71f9c19a42b1e468add83ccc69
diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
new file mode 100644
index 000000000000..4c7f124c5e3d
--- /dev/null
+++ b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
@@ -0,0 +1,12 @@
+diff -ur piler.orig/gff.cpp piler/gff.cpp
+--- piler.orig/gff.cpp	2004-12-18 01:25:29.000000000 +0200
++++ piler/gff.cpp	2009-08-09 17:22:33.000000000 +0300
+@@ -70,7 +70,7 @@
+ 		const char *Attrs = Fields[8];

+ 

+ 	// Truncate attrs if comment found

+-		char *Pound = strchr(Attrs, '#');

++		char *Pound = const_cast <char*> (strchr(Attrs, '#'));

+ 		if (0 != Pound)

+ 			*Pound = 0;

+ 

diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/piler/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/piler/piler-1.0.ebuild b/sci-biology/piler/piler-1.0.ebuild
new file mode 100644
index 000000000000..139f92cda50f
--- /dev/null
+++ b/sci-biology/piler/piler-1.0.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Analysis of repetitive DNA found in genome sequences"
+HOMEPAGE="http://www.drive5.com/piler/"
+#SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="|| ( sci-biology/muscle
+	sci-libs/libmuscle )
+	sci-biology/pals"
+
+S=${WORKDIR}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+}
+
+src_compile() {
+	emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
+}
+
+src_install() {
+	dobin piler
+}