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

3 files changed, 48 insertions, 0 deletions

diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
new file mode 100644
index 000000000000..1275fda8b314
--- /dev/null
+++ b/sci-biology/phrap/Manifest
@@ -0,0 +1 @@
+DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/phrap/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/phrap/phrap-1.080812-r1.ebuild b/sci-biology/phrap/phrap-1.080812-r1.ebuild
new file mode 100644
index 000000000000..d6864dc373cb
--- /dev/null
+++ b/sci-biology/phrap/phrap-1.080812-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Shotgun assembly and alignment utilities"
+HOMEPAGE="http://www.phrap.org/"
+SRC_URI="phrap-${PV}-distrib.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	dev-lang/perl
+	dev-perl/perl-tk"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
+	einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\""
+	einfo "and put it in ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die
+	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die
+}
+
+src_install() {
+	dobin cross_match loco phrap phrapview swat
+	newbin cluster cluster_phrap
+	for i in {general,phrap,swat}.doc ; do
+		newdoc ${i} ${i}.txt
+	done
+}