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, 157 insertions, 0 deletions

diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
new file mode 100644
index 000000000000..756ab900c480
--- /dev/null
+++ b/sci-biology/bioperl/Manifest
@@ -0,0 +1 @@
+DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild
new file mode 100644
index 000000000000..afaa8236b5a2
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+MY_PN=BioPerl
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.6.901
+inherit perl-module
+
+SUBPROJECTS="+db +network +run"
+MIN_PV=$PV
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
+
+REQUIRED_USE="minimal? ( !graphviz )"
+
+CDEPEND="
+	dev-perl/libwww-perl
+	!minimal? (
+		dev-perl/Algorithm-Munkres
+		dev-perl/Array-Compare
+		dev-perl/yaml
+		dev-perl/Bio-ASN1-EntrezGene
+		dev-perl/Clone
+		dev-perl/Convert-Binary-C
+		dev-perl/Data-Stag
+		dev-perl/GD
+		dev-perl/Graph
+		>=dev-perl/HTML-Parser-3.60
+		dev-perl/List-MoreUtils
+		dev-perl/Math-Random
+		dev-perl/PostScript
+		dev-perl/set-scalar
+		dev-perl/SOAP-Lite
+		dev-perl/Sort-Naturally
+		dev-perl/Spreadsheet-ParseExcel
+		>=virtual/perl-Storable-2.05
+		>=dev-perl/SVG-2.26
+		>=dev-perl/SVG-Graph-0.01
+		dev-perl/URI
+		>=dev-perl/XML-DOM-XPath-0.13
+		dev-perl/XML-Parser
+		>=dev-perl/XML-SAX-0.15
+		dev-perl/XML-Simple
+		dev-perl/XML-Twig
+		>=dev-perl/XML-Writer-0.4
+		dev-perl/XML-DOM
+		dev-perl/XML-XPath
+	)
+	graphviz? ( dev-perl/GraphViz )
+	sqlite? ( dev-perl/DBD-SQLite )"
+DEPEND="dev-perl/Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+	network? ( >=sci-biology/bioperl-network-${MIN_PV} )
+	run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
new file mode 100644
index 000000000000..1cf70db6b533
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit perl-module git-2
+
+SUBPROJECTS="+db +network +run"
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="git://github.com/${PN}/${PN}-live.git
+	https://github.com/${PN}/${PN}-live.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="-minimal graphviz ${SUBPROJECTS}"
+
+CDEPEND="
+	dev-perl/Data-Stag
+	dev-perl/libwww-perl
+	!minimal? (
+		dev-perl/Ace
+		dev-perl/Bio-ASN1-EntrezGene
+		dev-perl/Spreadsheet-ParseExcel
+		dev-perl/Spreadsheet-WriteExcel
+		>=dev-perl/XML-SAX-0.15
+		dev-perl/Graph
+		dev-perl/SOAP-Lite
+		dev-perl/Array-Compare
+		dev-perl/SVG
+		dev-perl/XML-Simple
+		dev-perl/XML-Parser
+		dev-perl/XML-Twig
+		>=dev-perl/HTML-Parser-3.60
+		>=dev-perl/XML-Writer-0.4
+		dev-perl/Clone
+		dev-perl/XML-DOM
+		dev-perl/set-scalar
+		dev-perl/XML-XPath
+		dev-perl/XML-DOM-XPath
+		dev-perl/Algorithm-Munkres
+		dev-perl/Data-Stag
+		dev-perl/Math-Random
+		dev-perl/PostScript
+		dev-perl/Convert-Binary-C
+		dev-perl/SVG-Graph
+	)
+	graphviz? ( dev-perl/GraphViz )"
+DEPEND="dev-perl/Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
+	db? ( >=sci-biology/bioperl-db-${PV} )
+	network? ( >=sci-biology/bioperl-network-${PV} )
+	run? ( >=sci-biology/bioperl-run-${PV} )"
+
+S="${WORKDIR}/BioPerl-${PV}"
+
+src_configure() {
+	sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
+		-e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \
+		-e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \
+		|| die
+	if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
+	perl-module_src_configure
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
new file mode 100644
index 000000000000..210ba364d45f
--- /dev/null
+++ b/sci-biology/bioperl/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>
+  <use>
+    <flag name="run">Install sci-biology/bioperl-run</flag>
+    <flag name="network">Install sci-biology/bioperl-run</flag>
+    <flag name="db">Install sci-biology/bioperl-run</flag>
+  </use>
+  <upstream>
+    <remote-id type="cpan">BioPerl</remote-id>
+  </upstream>
+</pkgmetadata>