sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)

(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)

1 files changed, 158 insertions, 0 deletions

diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.33.ebuild
new file mode 100644
index 000000000..e2bcfc3be
--- /dev/null
+++ b/sci-biology/gbrowse/gbrowse-2.33.ebuild
@@ -0,0 +1,158 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+EAPI="2"
+
+inherit perl-module webapp
+
+MY_P="GBrowse-${PV}"
+
+DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org"
+# mirror://sourceforge/gmod/${MY_P}.tar.gz
+# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
+SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz
+	test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
+			http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
+
+LICENSE="Artistic"
+# webapp ebuilds do not set SLOT
+KEYWORDS="~x86 ~amd64"
+IUSE="-minimal svg test" # lwp moby scf
+
+S="${WORKDIR}/${MY_P}"
+
+# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
+# TODO: make sure www-servers/apache +cgi
+DEPEND="
+	>=perl-core/Module-Build-0.380.0
+	>=dev-lang/perl-5.8.8
+	dev-perl/Capture-Tiny
+	>=sci-biology/bioperl-1.6
+	>=dev-perl/GD-2.07
+	dev-perl/IO-String
+	virtual/perl-Digest-MD5
+	>=dev-perl/CGI-Session-4.03
+	dev-perl/Statistics-Descriptive
+	>=dev-perl/Bio-Graphics-1.97
+	>=dev-perl/JSON-2.510.0
+	dev-perl/libwww-perl
+	svg? ( dev-perl/GD-SVG )"
+
+# TODO: based on the following message in apache/error_log the list of deps should be longer
+# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
+
+#    *  Bio::DB::BigFile is not installed
+#    *  Bio::DB::Sam is not installed
+#    *  DBD::Pg is not installed
+
+
+RDEPEND="${DEPEND}
+	>=www-servers/apache-2.0.47
+	www-apache/mod_fastcgi
+	dev-perl/DBI
+	|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
+	!minimal? (
+		dev-perl/File-NFSLock
+		dev-perl/FCGI
+		perl-core/Math-BigInt
+		perl-core/Math-BigInt-FastCalc
+		dev-perl/Math-BigInt-GMP
+		dev-perl/Digest-SHA1
+		dev-perl/Crypt-SSLeay
+		dev-perl/Net-SMTP-SSL
+		dev-perl/Net-OpenID-Consumer
+		virtual/perl-DB_File
+		dev-perl/DB_File-Lock
+		dev-perl/GD-SVG
+		dev-perl/Text-Shellwords
+		dev-perl/XML-Twig
+		dev-perl/XML-DOM
+		dev-perl/XML-Writer
+		dev-perl/XML-Parser
+		dev-perl/Bio-Das
+		dev-perl/Text-Shellwords
+	)"
+
+src_prepare() {
+	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
+	sed -i 's/process_/bp_process_/g' INSTALL || die
+	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
+}
+
+src_configure() {
+	# GBROWSE_ROOT is the root path in SRC_URI to be prepended
+	# /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
+	webapp_src_preinst
+	perl Makefile.PL \
+		HTDOCS="${MY_HTDOCSDIR}" \
+		CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
+		CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
+		PACKAGE_DIR="${D}" \
+		INSTALLDIRS=vendor \
+		GBROWSE_ROOT="gbrowse" \
+		DESTDIR="${D}" \
+		DATABASES="/var/www/gbrowse2/databases/" \
+		TMP="/var/tmp/gbrowse2" \
+		INSTALLETC="n" \
+		INSTALLCONF="n" \
+		WWWUSER="apache" \
+		DO_XS=1 \
+		NONROOT=1 \
+		|| die
+}
+
+src_install() {
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install
+
+	# TODO: write our own readme
+	webapp_postinst_txt en "${S}"/INSTALL
+	webapp_src_install || die "Failed running webapp_src_install"
+
+	# should create a /etc/init.d/ startup script based on this
+	# /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
+
+	chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die
+
+	mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
+	ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die
+
+	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 "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
+
+	sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
+	sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
+	sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
+}
+
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+
+	einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database"
+	einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
+}
+
+src_test() {
+	mysql -uroot -p password -e 'create database yeast'
+	mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'
+	mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost'
+	mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'
+
+	cd /usr/portage/distfiles || die
+	gzip -d yeast.fasta.gz || die
+	gzip -d yeast.gff.gz || die
+	#gzip -d fly.fasta.gz
+	#gzip -d fly.gff.gz
+	bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die
+}