reinit the tree, so we can have metadata

1 files changed, 84 insertions, 0 deletions

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 $?
+}