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, 46 insertions, 0 deletions

diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
new file mode 100644
index 000000000000..92cfe6ce81b8
--- /dev/null
+++ b/sci-biology/phred/Manifest
@@ -0,0 +1 @@
+DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975
diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/phred/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/phred/phred-071220.ebuild b/sci-biology/phred/phred-071220.ebuild
new file mode 100644
index 000000000000..22600ba92c50
--- /dev/null
+++ b/sci-biology/phred/phred-071220.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A base caller for Sanger DNA sequencing"
+HOMEPAGE="http://phrap.org/phredphrapconsed.html"
+SRC_URI="phred-dist-071220.b-acd.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	elog "Please visit ${HOMEPAGE} and obtain the file"
+	elog "${SRC_URI}, then place it in ${DISTDIR}"
+}
+
+src_compile() {
+	sed -i -e 's/CFLAGS=/CFLAGS += /' Makefile
+	emake daev || die
+	emake || die
+}
+
+src_install() {
+	dobin phred daev || die
+	insinto /usr/share/${PN}
+	doins phredpar.dat || die
+	echo "PHRED_PARAMETER_FILE=/usr/share/${PN}/phredpar.dat" > 99phred
+	doenvd 99phred || die
+	newdoc DAEV.DOC DAEV.DOC.txt
+	newdoc PHRED.DOC PHRED.DOC.txt
+}