GBrowse-2.39.ebuild

GBrowse-2.39.ebuild (text/plain), 5.04 KB, created by Martin Mokrejš on 2011-08-02 01:37:26 UTC

# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/GBrowse/GBrowse-2.39.ebuild,v 1.1 2011/07/20 00:56:03 weaver Exp $

EAPI=4

MODULE_AUTHOR=LDS
inherit perl-module webapp

DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser"
HOMEPAGE="http://gmod.org/wiki/GBrowse"
KEYWORDS="~amd64 ~x86"
IUSE="-minimal mysql pdf postgres +sqlite svg xml"

# sci-biology/ucsc-genome-browser provides bigWig.h and jkweb.a, aka "Jim Kent's src"
CDEPEND=">=sci-biology/bioperl-1.6.9
	>=dev-perl/Bio-Graphics-2.09
	>=dev-perl/GD-2.07
	>=dev-perl/CGI-Session-4.02
	dev-perl/IO-String
	perl-core/Math-BigInt
	perl-core/Math-BigInt-FastCalc
	dev-perl/Math-BigInt-GMP
	virtual/perl-Digest-MD5
	dev-perl/Digest-SHA1
	>=dev-perl/JSON-2.510.0
	dev-perl/libwww-perl
	dev-perl/Statistics-Descriptive
	!minimal? (
		dev-perl/Bio-Das
		>=dev-perl/Bio-SamTools-1.29
		>=dev-perl/Bio-DB-Das-Chado-0.32
		virtual/perl-DB_File
		dev-perl/DB_File-Lock
		dev-perl/File-NFSLock
		>=dev-perl/Bio-BigFile-1.00
		dev-perl/DBI
		mysql? ( dev-perl/DBD-mysql )
		postgres? ( dev-perl/DBD-Pg )
		sqlite? ( dev-perl/DBD-SQLite )
		dev-perl/FCGI
		svg? ( dev-perl/GD-SVG )
		pdf? ( media-gfx/inkscape )
		dev-perl/Crypt-SSLeay
		dev-perl/Net-OpenID-Consumer
		dev-perl/Net-SMTP-SSL
		dev-perl/Text-Shellwords
		>=dev-perl/Text-ParseWords-3.27
	xml? ( dev-perl/XML-Twig
		dev-perl/XML-DOM
		dev-perl/XML-Writer
		dev-perl/XML-Parser )
		sci-biology/ucsc-genome-browser
	)" # - requires jklib to compile
DEPEND=">=virtual/perl-Module-Build-0.380.0
	dev-perl/Capture-Tiny
	dev-perl/TermReadKey
	perl-core/File-Temp
	${CDEPEND}"
RDEPEND="${CDEPEND}
	www-servers/apache"

PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-${PV}.patch )

src_configure() {
	webapp_src_preinst

#	myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse"
	myconf="--conf=/etc/gbrowse2"
	myconf="${myconf} --htdocs=${MY_HTDOCSDIR}"
	myconf="${myconf} --cgibin=${MY_CGIBINDIR}"
	myconf="${myconf} --tmp=/var/tmp/gbrowse2"
	myconf="${myconf} --persistent=/var/db/gbrowse2"
	myconf="${myconf} --databases=/var/db/gbrowse2/databases"
	myconf="${myconf} --installconf=no"
	myconf="${myconf} --installetc=no"
	myconf="${myconf} --wwwuser=apache"
	NONROOT=1 DO_XS=1 perl-module_src_configure
}

src_install() {
	perl-module_src_install

	dodir /var/tmp/gbrowse2 # do not prepend "${D}", that is done automagically
	dodir /var/db/gbrowse2/sessions # do not prepend "${D}", that is done automagically
	dodir /var/db/gbrowse2/userdata # do not prepend "${D}", that is done automagically

	# pre-create a link to a cache directory with server-generated images so that
	#   webapp-config will carry it forward
	# the "gbrowse2" here should match the "gbrowse2" on the
	#   '/usr/sbin/webapp-config -I -h localhost -u root -d /gbrowse2 ...' line
	dodir /var/www/localhost/htdocs/gbrowse2
	dodir /var/tmp/gbrowse2
	dosym /var/tmp/gbrowse2/images /var/www/localhost/htdocs/gbrowse2/i

	# for some reason some generated links point to /cgi-bin/gb2/gbrowse, so fix that
	# the bug is in /etc/gbrowse2/yeast_chr1+2.conf and /etc/gbrowse2/yeast_renderfarm.conf
	# the following link does not fix it unless you loosened your webserver settings
	# and added FollowSymlinks for the cgi-bin directory but let's give it a chance
	dosym /var/www/localhost/cgi-bin /var/www/localhost/cgi-bin/gb2

	# pre-create the file so that gbrowse_metadb_config.pl when run as
	# root does not create it with root.root ownership
	touch "${D}"/var/db/gbrowse2/sessions/cgisess.db

	webapp_serverowned -R /var/tmp/gbrowse2 # do not prepend "${D}", that is done automagically
	webapp_serverowned -R /var/db/gbrowse2

	webapp_src_install

	# TODO: write our own readme
	webapp_postinst_txt en "${S}"/INSTALL

	# TODO: should create a /etc/init.d/ startup script based on this
	# "${S}"/etc/init.d/gbrowse-slave
}

pkg_postinst() {
	/usr/bin/gbrowse_metadb_config.pl

	# the above webapp_serverowned() does not actually work, fix the ownerships
	chown -R apache.apache /var/tmp/gbrowse2 /var/db/gbrowse2

	einfo "Please run '/usr/sbin/webapp-config -I -h localhost -u root -d /gbrowse2 GBrowse 2.39'."
	einfo "Probably you want to install a cron job to remove the generated temporary images:"
	einfo "  find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}"
	einfo "I did not need any /etc/apache2/vhosts.d/gbrowse.conf but you may find one sample"
	einfo "  in ${FILESDIR}/gbrowse.conf.vhosts.d"
	einfo "The application creates&writes e.g. /var/db/gbrowse2/databases/yeast_scaffolds/directory.index"
	einfo "  and /var/db/gbrowse2/sessions.db.lck files under apache.apache ownership. Be sure"
	einfo "  when you run gbrowse_metadb_config.pl or other tools as root that they did not create"
	einfo "  new files under /var/db/gbrowse2/ or /var/tmp/gbrowse2/ , GBrowse will then have"
	einfo "  problem to modify/delete them."
	einfo "If you uninstall the package you may also want to do: 'rm -rf /var/db/gbrowse2 /var/tmp/gbrowse2'"
}

pkg_postrm() {
	einfo "You may also want to do: 'rm -rf /var/db/gbrowse2 /var/tmp/gbrowse2'"
}