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, 55 insertions, 0 deletions

diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest
new file mode 100644
index 000000000000..d9522e5cccb5
--- /dev/null
+++ b/sci-biology/transfac/Manifest
@@ -0,0 +1 @@
+DIST transfac32.tar.Z 3346266 RMD160 892164634a80f388ba3c588823576ff0b5582338 SHA1 1f950c981364b03819463536c8d0195fe7351f02 SHA256 cf5c64e6f23037d73562d66f9dde56a767a8f31974a1c0906ec68edea3731a7f
diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml
new file mode 100644
index 000000000000..d07df4fd4dbf
--- /dev/null
+++ b/sci-biology/transfac/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		TRANSFAC® is a database of eukaryotic transcription factors, of their
+		genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old
+		public version available at the European Bioinformatics Institute.
+		TRANSFAC® is currently maintained by the BIOBASE company. Altough they
+		offer public access to a more recent version of the database, they
+		offer no free downloadable version.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/transfac/transfac-3.2.ebuild b/sci-biology/transfac/transfac-3.2.ebuild
new file mode 100644
index 000000000000..e2cdd68565f2
--- /dev/null
+++ b/sci-biology/transfac/transfac-3.2.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="A database of eucaryotic transcription factors"
+HOMEPAGE="http://www.gene-regulation.com/pub/databases.html"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z"
+LICENSE="public-domain"
+
+SLOT="3"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="emboss minimal"
+# Minimal build keeps only the indexed files (if applicable) and the documentation.
+# The non-indexed database is not installed.
+
+DEPEND="emboss? ( sci-biology/emboss )"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_compile() {
+	if use emboss; then
+		echo
+		einfo "Indexing TRANSFAC for usage with EMBOSS."
+		EMBOSS_DATA=. tfextract -auto -infile class.dat  || die \
+			"Indexing TRANSFAC failed."
+		echo
+	fi
+}
+
+src_install() {
+	if ! use minimal; then
+		insinto /usr/share/${PN}-${SLOT}
+		doins *.dat || die
+	fi
+	if use emboss; then
+		insinto /usr/share/EMBOSS/data
+		doins tf* || die
+	fi
+}