reinit the tree, so we can have metadata

4 files changed, 162 insertions, 0 deletions

diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
new file mode 100644
index 000000000000..d4fd5b9c45c0
--- /dev/null
+++ b/sci-biology/bioperl/Manifest
@@ -0,0 +1,6 @@
+DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd
+EBUILD bioperl-1.6.9.ebuild 1544 SHA256 48af54169e933b299b5cbccb8d024c622ce54b16b16c2b81de60eb8a50e30dbf SHA512 2e6167abb3ab729eef114ef9e38955e5d2b5353efaf86f5af16aa00348a661adc5b2297f22c2a77126c7f4f3f08f3db9c0af4210ddb3328653f11b1f5a782744 WHIRLPOOL c44238e73089079e645711b59e2ca75071ed0c92b193fe5990ba2a72d1b06b8c80d85ed73921883a92be04b61144b1f600796e6d210b7477b6bc7af74bc609ba
+EBUILD bioperl-9999-r1.ebuild 1793 SHA256 4572481f8dcf47e793219278f5c745861d6142c469e2bc337a703b636674f53b SHA512 25459e6fdeacb6bded0c81a4bbd3a6d85f7cbae973b6f9b8a2ee1a44ab56b5a81556b1c6176e389e57efa660fdb35a6b61c71aca65f90e221bc04a0dda395e5c WHIRLPOOL 2a78b548458705effdc5cdedef1615933643415548ab47d75c7735fb212307378107709a4d47748993ea534b7ec85619bf1f6df4d522a280a206405951297530
+MISC ChangeLog 3082 SHA256 922b31d7106a75064fc95c36bee21e8674e13efa8922d9d48a5c992c822517bf SHA512 b3af13290548dbd7d06a468b1c7cda939861bae04813d69e88f8a7e48ef191757b6315375c25d4e88932cf4a890fd6851f23c97e537f35913262be26fa40ca25 WHIRLPOOL 9f0b7b6dc145e0001cfc628e353f3e7a1f825b6da378bc8a0dc725889cefdd83e33a8095b76c17f03e7475e4d54047130a815eeb20baae530556c2870186980a
+MISC ChangeLog-2015 10092 SHA256 c62eae3a76746911bc6ba9682db44cae7205fab5fbde5e04f6ff55c22b5d55c6 SHA512 dc29fc462dc9b6c9d0dfe57c7e594b7d12da79aa12382e0ac738a48c470e0051ecac32b15c1af79d68183798050a2d09ebed07e8bbd78305ffa5cee4a3fba657 WHIRLPOOL 657e7f90335f20d92a4eea80d606464e279a282b85603c12b289e446204d00f6e02aa6b761fac0802a3f95ebd4f5ea38adb7e1a9ec9b1c53e1b16e9a4adb74af
+MISC metadata.xml 541 SHA256 83910a66da15199aa7cc29e9fca93cea8bfd8edb96f9efdf549dcf6c8ea3fa2e SHA512 0693aba25e02d3ad67f82c2c77f9987ae06cb6545bb58df2c57f076a22d5c2f6d15c7fdc11b0766748680d53c709c7682b53f866a4f45d7d8a875d1311277e5c WHIRLPOOL b6359f4f497274340afabe6c6e83290c4be0c58b48598216061cc5f81c8a8ba263e2bc408fd2d00a4450bf3750091ad5d01e6321c7843c3cb4d73a993df101de
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..d2519a0d30b6
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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-${MIN_PV} )"
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
new file mode 100644
index 000000000000..f166946c008f
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="5"
+
+inherit perl-module git-2
+
+SUBPROJECTS="+db +network +run"
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/${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..1cd5db0e9619
--- /dev/null
+++ b/sci-biology/bioperl/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <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>