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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit eutils perl-module webapp
MY_P="GBrowse-${PV}"
DESCRIPTION="Display of genomic annotations on interactive web pages"
HOMEPAGE="http://gmod.org/"
# mirror://sourceforge/gmod/${MY_P}.tar.gz
# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
SRC_URI="
mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
test? (
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
LICENSE="Artistic"
# webapp ebuilds do not set SLOT
KEYWORDS="~x86 ~amd64"
IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf
S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="!!sci-biology/GBrowse
>=virtual/perl-Module-Build-0.380.0
>=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
>=dev-perl/GD-2.07
dev-perl/IO-String
virtual/perl-Digest-MD5
>=dev-perl/CGI-Session-4.03
dev-perl/Statistics-Descriptive
>=dev-perl/Bio-Graphics-2.26
>=dev-perl/JSON-2.510.0
dev-perl/TermReadKey
dev-perl/libwww-perl
svg? ( dev-perl/GD-SVG )
pdf? ( media-gfx/inkscape )
mysql? ( dev-perl/DBD-mysql )
postgres? ( dev-perl/DBD-Pg )
sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
# TODO: based on the following message in apache/error_log the list of deps should be longer
# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
fastcgi? ( dev-libs/fcgi )
www-apache/mod_fastcgi
dev-perl/DBI
|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
!minimal? (
dev-perl/File-NFSLock
dev-perl/FCGI
virtual/perl-Math-BigInt
virtual/perl-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
postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
>=dev-perl/Bio-SamTools-1.29
>=dev-perl/Bio-BigFile-1.06
<=sci-biology/primer3-2
)"
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
epatch \
"${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
"${FILESDIR}"/destdir.patch \
"${FILESDIR}"/fix-PNG-export.patch \
"${FILESDIR}"/symlink.patch \
"${FILESDIR}"/gbrowse_metadb_config.pl.patch \
"${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
Changes; do
sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f"
done
for f in htdocs/index.html; do
sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f"
done
}
src_configure() {
# GBROWSE_ROOT is the root path in SRC_URI to be prepended
# /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
webapp_src_preinst
perl Makefile.PL \
HTDOCS="${MY_HTDOCSDIR}" \
CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
PACKAGE_DIR="${D}" \
INSTALLDIRS=vendor \
GBROWSE_ROOT="gbrowse" \
DESTDIR="${D}" \
DATABASES="/var/db/gbrowse2/databases" \
PERSISTENT="/var/db/gbrowse2" \
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 "${S}"/INSTALL
webapp_src_install || die "Failed running webapp_src_install"
# should create a /etc/init.d/ startup script based on this
# /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
mkdir -p "${D}"/var/tmp/gbrowse2/images
chown -R apache.apache "${D}"/var/tmp/gbrowse2
# mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
# ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die
# whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise:
# 1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck
# [no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well]
# 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get
# [Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/
mkdir -p "${D}"/var/db/gbrowse2
mkdir -p "${D}"/var/db/gbrowse2/databases
mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata
chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache
einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
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 do"
einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf"
sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
}
pkg_postinst() {
webapp_pkg_postinst || die "webapp_pkg_postinst failed"
einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
einfo "Fix also the other copy of the file:"
einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
}
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
}
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