reinit the tree, so we can have metadata

6 files changed, 232 insertions, 0 deletions

diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest
new file mode 100644
index 000000000000..6cb8843176a4
--- /dev/null
+++ b/sci-biology/bioperl-db/Manifest
@@ -0,0 +1,8 @@
+AUX bioperl-db-1.6.9-db.patch 1567 SHA256 8ae757084e0f2b1933da271921ede70bed2a0408c179108b62520b2433a4f493 SHA512 a0a2ca951645b70b2e4eb3390598b2a42d6631109500238d6fc482d97a616ec1881738e5dc9af118d37fdf50657916ff275124f409510cf15515dfbc829766c0 WHIRLPOOL 0e5eaeed9248ca9581e4ed20f8ad616e12947e75e97f6ee4d0ded580d74c1a606a78b8352337c7accd42e3f5709e602c4694f97e44a9ef106fce57343bdd8cea
+DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2
+EBUILD bioperl-db-1.6.9-r1.ebuild 2024 SHA256 58f6b9583d0f68d1cce6cdf6093719aa384f96be474b3694bc83e5e89d28a9f3 SHA512 91814c0b622e2390ac3db18bed47d4ea5f02f7fe493a668bab9a5de4ec3735c64385d4b11ca21d34a05f476e30b7fce7100b3fab77d51607b78804f9b23451e0 WHIRLPOOL d95ba2f87c25536d5ebdcfe89fa7eeb127c07fd2429b01647e3fa5f54d064120fc27f4bc089e1237035baf70245c07ffa5e2cbf318cf5cc998947ec3c775352e
+EBUILD bioperl-db-1.6.9.ebuild 914 SHA256 3a4b5008b5fba0376a25b252fbe860c585922a9c6161bc1038f7262d2746050b SHA512 0d555ef35d5a6e9fda3a48ffc3c7437ad52110c8c9f2a223f103c15c6a866c6c776b7c8d0b1c5c1848336263c64a6e79f80ba476d6205e8f3a90788236ff13e8 WHIRLPOOL 01cb04c656c944eb23b3d3c741e887663b6605872b612c134a6a89129460eb3241d5f731bf4d84fb06acc5f6df6be64dcfba54156854ba1e8208fbdac2ac65c4
+EBUILD bioperl-db-9999-r1.ebuild 811 SHA256 81ad8e871f3da8ce9e8135baaf69d5d07b13fedc8bd5a2b2912a3367580b24fa SHA512 23c57f3cf36d0be73470941b408ef59e84457b9db37cb764ba9553bb38404c48498665982a827c981328b6e37b8e7429170644a51ef3d8e9bbd2fe468f8ca7d8 WHIRLPOOL b40c5193ff19433435dbd7fca3ac0018c6e0d91f05f46b7f8dacb0bfac70ca34407f148a9ade41650562c3e7d0a78793c645adfc9d3f0242dec09ceb610af303
+MISC ChangeLog 2501 SHA256 eb07657ab421bb85f4f77009b0e5918ad4752a507e79bcfb166d7cbe1dc6e49a SHA512 d71c1f72dc281a5c1bfdc9f706cabd8e12816094a2481d79f48d37b0444b42801becefc7a94a7d0867498f618b80b873ad77256e4469cb55353ea46e281eb3e4 WHIRLPOOL b58d0a4f108826b26b2953005629e74fc1da6640877104988a842b04fa0ca3bb6dc36b6d73f3ac42b8c23da5a6e1b4844c06160e77c812029b37ae469497140e
+MISC ChangeLog-2015 2319 SHA256 cc5e31c7b46436054b18d1d2b6d020c68080dc59e9c807857e81fbfbdf72a1ef SHA512 dc3f7e0d92bd8984a83aed5a5fe739f24cf2e96f53087af0f6d36c6a441102733f109c22da0e960c8b2815a133b99a2129c448077e36f7a5f9a368386f302aa5 WHIRLPOOL 62459d94d25fcbe5ccfdc3ffb4316600acd1389cb2ebaebc927f2680e8aca56d955ff2cb02183cb754efc048e6fd751108fed81aba97683573f383ce0f1b69d1
+MISC metadata.xml 344 SHA256 1b450924ccc444666839a3700e9ac18a38f8f99db0cbeedd5f4e202466edd564 SHA512 a477289255247669c332915665c4d414ba2857b5716a60e8aec1bf8d1c38009c9fcfb7421a02bdbd9ad566be32bf2b21f57fd21c745aa62185d5dcd13d78bf70 WHIRLPOOL e29a2e18f1d081a4624730b992858c71d1124a7c320b76cdbb2ec422f3071c67c6a0cc0d14aa0c731fec643a5f44270f67441913b8b26f454677bc9aa5a9e2f4
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
new file mode 100644
index 000000000000..facab7d5ffbe
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
@@ -0,0 +1,84 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+BIOPERL_RELEASE=1.6.9
+
+DIST_NAME=BioPerl-DB
+DIST_AUTHOR=CJFIELDS
+DIST_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+IUSE="test"
+
+DIST_TEST="do" # Parallelism probably bad
+PATCHES=( "${FILESDIR}/${PN}-1.6.9-db.patch" )
+RDEPEND="
+	>=sci-biology/bioperl-${PV}
+	dev-perl/DBD-mysql
+	dev-perl/DBI
+	sci-biology/biosql"
+DEPEND="${RDEPEND}
+	dev-perl/Module-Build
+	test? (
+		dev-perl/Data-Stag
+		dev-perl/Sub-Uplevel
+		dev-perl/Test-Warn
+		dev-perl/Test-Exception
+		virtual/perl-Test-Simple
+	)
+"
+src_prepare() {
+	export GENTOO_DB_HOSTNAME=localhost
+	perl-module_src_prepare
+}
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
+src_test() {
+	einfo "Removing bundled test libraries t/lib"
+	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
+
+	ebegin "Setting up test database"
+
+	local mysqld="${EPREFIX}/usr/sbin/mysqld"
+	local socket="${T}/mysql.sock"
+	local pidfile="${T}/mysql.pid"
+	local datadir="${T}/mysql-data-dir"
+	local mysql="${EPREFIX}/usr/bin/mysql"
+
+	mkdir -p "${datadir}" || die "Can't make mysql database dir";
+	chmod 755 "${datadir}" || die "Can't fix mysql database dir perms";
+
+	if $mysqld --help | grep -q MariaDB ; then
+		"${EPREFIX}"/usr/share/mysql/scripts/mysql_install_db \
+			--basedir="${EPREFIX}/usr" \
+			--datadir="${datadir}" \
+			--user=$(whoami) || die "Can't initalize database"
+	fi
+
+	${mysqld} --no-defaults	--user=$(whoami) --skip-networking \
+							--socket="${socket}" \
+							--pid-file="${pidfile}" \
+							--datadir="${datadir}" &
+	maxtry=20
+	while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do
+		maxtry=$((${maxtry}-1))
+		echo -n "."
+		sleep 1
+	done
+	eend $?
+	export MYSQL_UNIX_PORT="${socket}"
+	perl-module_src_test
+	ebegin "Shutting down mysql test database"
+	pkill -F "${pidfile}"
+	eend $?
+}
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
new file mode 100644
index 000000000000..e6f0c45958a9
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="5"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-DB
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="test"
+RESTRICT="test"
+SRC_TEST="do"
+
+CDEPEND="
+	>=sci-biology/bioperl-${PV}
+	dev-perl/DBD-mysql
+	dev-perl/DBI
+	sci-biology/biosql"
+DEPEND="${CDEPEND}
+	dev-perl/Module-Build
+	test? (
+		dev-perl/Data-Stag
+		dev-perl/Sub-Uplevel
+		dev-perl/Test-Warn
+		dev-perl/Test-Exception
+		virtual/perl-Test-Simple
+	)
+"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
+src_test() {
+	einfo "Removing bundled test libraries t/lib"
+	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
+	perl-module_src_test
+}
diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
new file mode 100644
index 000000000000..2575b8c6af71
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="5"
+
+inherit perl-module git-2
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/bioperl/${PN}.git"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+	dev-perl/DBI
+	sci-biology/biosql"
+DEPEND="dev-perl/Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+S="${WORKDIR}/BioPerl-db-${PV}"
+
+src_configure() {
+	# This disables tests. TODO: Enable tests
+	sed -i -e '/biosql_conf();/d' \
+		-e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die
+	perl-module_src_configure
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
new file mode 100644
index 000000000000..36698651c7d1
--- /dev/null
+++ b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
@@ -0,0 +1,45 @@
+From d689a1473977b0aa368590ba1f913521e4f466c7 Mon Sep 17 00:00:00 2001
+From: Kent Fredric <kentfredric@gmail.com>
+Date: Tue, 18 Jul 2017 16:02:26 +1200
+Subject: [PATCH] Allow custom host/port configurations
+
+---
+ Build.PL           | 4 ++--
+ t/DBTestHarness.pm | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index ecc402e..a61190f 100755
+--- a/Build.PL
++++ b/Build.PL
+@@ -97,9 +97,9 @@ sub biosql_conf {
+         or die "Error: could not write to config file '$config_file'\n";
+     
+     my %config = (driver     => $drivers[0],
+-                  host       => '127.0.0.1',
++                  host       => $ENV{GENTOO_DB_HOSTNAME} || '127.0.0.1',
+                   user       => 'root',
+-                  port       => 3306,
++                  port       => $ENV{GENTOO_DB_PORT} || undef,
+                   password   => '',
+                   dbname     => 'bioseqdb',
+                   database   => 'biosql',
+diff --git a/t/DBTestHarness.pm b/t/DBTestHarness.pm
+index b660429..91e0c54 100755
+--- a/t/DBTestHarness.pm
++++ b/t/DBTestHarness.pm
+@@ -47,9 +47,9 @@ my $counter=0;
+ # Default settings as a hash
+ my $dflt = {
+     'driver'        => 'mysql',
+-    'host'          => 'localhost',
++    'host'          => $ENV{GENTOO_DB_HOST} || 'localhost',
+     'user'          => 'root',
+-    'port'          => undef,
++    'port'          => $ENV{GENTOO_DB_PORT} || undef,
+     'password'      => '',
+     'schema_sql'    => ['../biosql-schema/sql/biosqldb-mysql.sql'],
+     'database'      => 'biosql',
+-- 
+2.13.1
+
diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml
new file mode 100644
index 000000000000..09e1cb381b7f
--- /dev/null
+++ b/sci-biology/bioperl-db/metadata.xml
@@ -0,0 +1,11 @@
+<?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>
+  <upstream>
+    <remote-id type="cpan">BioPerl-DB</remote-id>
+  </upstream>
+</pkgmetadata>