Version bump and lots of ebuild improvements, it works for me now

7 files changed, 299 insertions, 1 deletions

diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest
index 732288501..0af49e2a7 100644
--- a/sci-biology/gbrowse/Manifest
+++ b/sci-biology/gbrowse/Manifest
@@ -1,6 +1,22 @@
+AUX GBrowseInstall.pm.patch 546 RMD160 a479d11e70b0c1340d50760e0f2aae5030b2aa26 SHA1 bac9d3692586c878b9a3f5a2df398e72bd73ede1 SHA256 0f4eaedce7f049628dc78ea2921bd1a5666981d77f54c6d240b1ae572f410c22
+AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66
+AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219
+AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21
 DIST GBrowse-2.00.tar.gz 3844690 RMD160 f3856ca620d8adc10172d8dfb644dfbbd25cbf88 SHA1 9d78393ca21d2569a975cfff7588cb7fe62d1082 SHA256 62c96ae1c6c1494ff67fbea1fde0d80d5051705c22167a55db317a0d33b1b8ea
+DIST GBrowse-2.03.tar.gz 11773792 RMD160 5f02c3f824ff6b0d2a32bbfb744be9bff71098a0 SHA1 92b6d4d43c663393f1a5a6b0283f0d740b2c0399 SHA256 279ec6546304888e506809bccefae9007e359e376a1abb643edfa30f7363574a
 DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486
+DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a
+DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af
+DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea
+DIST fly.gff.gz 18687640 RMD160 fb54c40dd9508d2f9e9cf24b65195cfbb70c8f82 SHA1 2d77f89f438b389fee7e7f5c92fc902eb1f99482 SHA256 db03b56993b739dd6e6df92dcb94163f04ca03a1911c99dd4df4fe65e16b6d44
+DIST human.gff.tar.gz 40362676 RMD160 ae0bb58667d01ebc4c0a34ede4d4b1c347bc42be SHA1 6d71aba7ef054291021bc340571c253ec71cd60f SHA256 7d0ea6363e6dda8618f53b42dea72d6ef6034b4f2fb541b94b4800383009f6b0
+DIST saccharomyces_cerevisiae.gff.bz2 4000445 RMD160 133a9076971958d4a242b6fc10869056c169e53e SHA1 8ef80023a0ccdc714742b628873ab06f06f0ebe4 SHA256 fb41705b64f0e36cbb46fb6b7557c2f36e517db582f1472d852f89b46ca750d4
+DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 ef8237f08b8380ce72c3c067120893087bc3bd21 SHA256 dbd6dcc44a8960e0e475b0be31b03caa3d97f4ddfc36ba566862732880f7dbc0
+DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f
+DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d
+DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1
 EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f
 EBUILD gbrowse-2.00.ebuild 1932 RMD160 5a0d15a10c2f6f9e4ac1f60ce048efcd2311cdb4 SHA1 186d5a91fbae9b6894091ac376addb84784d6a03 SHA256 21b035ef921900bc893a4de0fe123b6192860265e0594b73723c24b03dd5a23c
+EBUILD gbrowse-2.03.ebuild 5198 RMD160 b55f47213db96090869388c524b0505d709d9798 SHA1 0a050dc6a23998cd95ed65e8bd5c1d6fb91f2473 SHA256 49ab81d5ee5f33cd016618f3c17819731b91e75c759c877c3731a85d7c37424d
 MISC ChangeLog 1985 RMD160 9695d7522c6165b842087b67938629377f9cc82b SHA1 3edd2e74f9b26289d95ad7609b838edb3ccb9561 SHA256 76c1d0553f09390397af4354dc653677f25d06828e42e57a60b2f35a869222ac
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
new file mode 100644
index 000000000..e6163a732
--- /dev/null
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
@@ -0,0 +1,13 @@
+--- GBrowse-2.03/install_util/GBrowseInstall.pm.ori	2010-11-27 12:01:58.000000000 +0100
++++ GBrowse-2.03/install_util/GBrowseInstall.pm	2010-11-27 12:02:15.000000000 +0100
+@@ -436,8 +436,8 @@
+ 	$self->ownership_warning($databases,$user);
+     }
+ 
+-    chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+-    $self->fix_selinux;
++    # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
++    # $self->fix_selinux;
+ 
+     my $base = basename($self->install_path->{htdocs});
+ 
diff --git a/sci-biology/gbrowse/files/gbrowse-slave.default b/sci-biology/gbrowse/files/gbrowse-slave.default
new file mode 100755
index 000000000..46457c2dc
--- /dev/null
+++ b/sci-biology/gbrowse/files/gbrowse-slave.default
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+export PERL5LIB=$PERL5LIB
+
+DAEMON=$INSTALLSCRIPT/gbrowse_slave
+USER=$WWWUSER
+PRELOAD=$CONF/slave_preload.conf
+RUNDIR=/var/run/gbrowse
+LOGDIR=/var/log/gbrowse
+PORT="8101 8102 8103"
+VERBOSITY=3
+NICE=0
diff --git a/sci-biology/gbrowse/files/gbrowse-slave.init.d b/sci-biology/gbrowse/files/gbrowse-slave.init.d
new file mode 100755
index 000000000..c298faf3c
--- /dev/null
+++ b/sci-biology/gbrowse/files/gbrowse-slave.init.d
@@ -0,0 +1,94 @@
+#!/bin/sh
+### BEGIN INIT INFO
+# Provides:          gbrowse_slave
+# Required-Start:    $local_fs
+# Required-Stop:     $local_fs
+# Default-Start:     28
+# Default-Stop:      S
+# Short-Description: Start/Stop the gbrowse_slave rendering server.
+### END INIT INFO
+
+PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
+DAEMON=$INSTALLSCRIPT/gbrowse_slave
+NAME="gbrowse-slave"
+DESC="GBrowse slave track rendering server"
+
+test -x $DAEMON || exit 0
+set -e
+
+USER=$WWWUSER
+PRELOAD=""
+RUNDIR=/var/run/gbrowse
+LOGDIR=/var/log/gbrowse
+PORT='8101'
+VERBOSITY=1
+NICE=0
+
+if [ -f /etc/default/gbrowse-slave ]; then
+  . /etc/default/gbrowse-slave
+fi
+
+mkdir -p $RUNDIR
+chown -R $USER $RUNDIR
+mkdir -p $LOGDIR
+chown -R $USER $LOGDIR
+
+case "$1" in
+  start)
+	echo -n "Starting $DESC: $NAME "
+	for port in $PORT; do
+	    if test -e $RUNDIR/$NAME.$port.pid ; then
+		echo "$NAME already running, use restart instead."
+	    else
+                PRELOAD_DB=""
+		if [ "$PRELOAD" != "" ]; then
+                    PRELOAD_DB="--preload $PRELOAD"
+	        fi
+		ARGS="--port $port --verbose $VERBOSITY --log $LOGDIR/gbrowse_slave --pid $RUNDIR/$NAME.$port.pid $PRELOAD_DB"
+		su $USER -s /bin/sh -c "nice -n $NICE $DAEMON $ARGS"
+		echo -n "$port "
+	    fi
+	done
+	echo "."
+	;;
+  stop)
+	echo -n "Stopping $DESC: $NAME "
+	killed=0
+	for port in $PORT; do
+	    if test -e $RUNDIR/$NAME.$port.pid ; then
+		kill -TERM `cat $RUNDIR/$NAME.$port.pid`
+		killed=1
+	    fi
+            echo -n "$port "
+        done
+	if [ "$killed" -ne 1 ]; then
+	    base=`basename $DAEMON`
+	    killall -q -r $base || true
+        fi
+	echo "."
+	;;
+  status)
+       for port in $PORT; do
+               if test -e $RUNDIR/$NAME.$port.pid ; then
+                       kill -0 `cat $RUNDIR/$NAME.$port.pid`
+                       if [ "$?" -eq 0 ]; then
+                               echo "$NAME is running on port $port."
+                       fi
+               else
+                       echo "$NAME is not running on port $port."
+               fi
+       done
+       ;;
+  restart|force-reload)
+	$0 stop
+	sleep 3
+	$0 start
+	;;
+  *)
+	N=/etc/init.d/$NAME
+	echo "Usage: $N {start|stop|restart|force-reload|status}" >&2
+	exit 1
+	;;
+esac
+
+exit 0
diff --git a/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d b/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d
new file mode 100644
index 000000000..a3966ea19
--- /dev/null
+++ b/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d
@@ -0,0 +1,26 @@
+ScriptAlias /gbrowse/cgi-bin/gbrowse "/var/www/localhost/htdocs/gbrowse/cgi-bin/gbrowse"
+ScriptAlias /gbrowse/cgi-bin/ "/var/www/localhost/htdocs/gbrowse/cgi-bin/"
+
+<Directory "/var/www/localhost/htdocs/gbrowse/cgi-bin/">
+    Options ExecCGI
+    AllowOverride None
+    <IfModule mod_access.c>
+        Order allow,deny
+        Allow from all
+    </IfModule>
+</Directory>
+
+Alias /gbrowse/i "/var/www/localhost/htdocs/gbrowse/images"
+Alias /gbrowse "/var/www/localhost/htdocs/gbrowse"
+Alias /gbrowse2 "/var/www/localhost/htdocs/gbrowse"
+
+<Directory "/var/www/localhost/htdocs/gbrowse">
+    Options FollowSymlinks
+    AllowOverride None
+    <IfModule mod_access.c>
+        Order allow,deny
+        Allow from all
+    </IfModule>
+</Directory>
+
+
diff --git a/sci-biology/gbrowse/gbrowse-2.03.ebuild b/sci-biology/gbrowse/gbrowse-2.03.ebuild
new file mode 100644
index 000000000..9fc872b3d
--- /dev/null
+++ b/sci-biology/gbrowse/gbrowse-2.03.ebuild
@@ -0,0 +1,133 @@
+# 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-${PV}"
+
+DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org"
+SRC_URI="mirror://sourceforge/gmod/${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=">=dev-lang/perl-5.8.8
+	>=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
+	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
+
+RDEPEND="${DEPEND}
+	>=www-servers/apache-2.0.47
+	www-apache/mod_fastcgi
+	dev-perl/DBI
+	|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
+	!minimal? (
+		dev-perl/File-NFSLock
+		dev-perl/FCGI
+		perl-core/Math-BigInt
+		dev-perl/Digest-SHA1
+		dev-perl/Crypt-SSLeay
+		dev-perl/Net-SMTP-SSL
+		dev-perl/Net-OpenID-Consumer
+		virtual/perl-DB_File
+		dev-perl/DB_File-Lock
+		dev-perl/GD-SVG
+		dev-perl/Text-Shellwords
+		dev-perl/XML-Twig
+		dev-perl/XML-DOM
+		dev-perl/XML-Writer
+		dev-perl/XML-Parser
+		dev-perl/Bio-Das
+	)"
+
+src_prepare() {
+	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
+	sed -i 's/process_/bp_process_/g' INSTALL || die
+	epatch "${FILESDIR}"/GBrowseInstall.pm.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="${D}" \
+		DATABASES="/var/www/gbrowse2/databases/" \
+		TMP="/var/tmp/gbrowse2" \
+		INSTALLETC="n" \
+		INSTALLCONF="n" \
+		WWWUSER="apache" \
+		DO_XS=1 \
+		|| die
+}
+
+src_install() {
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install
+
+	# TODO: write our own readme
+	webapp_postinst_txt en "${S}"/INSTALL
+	webapp_src_install
+
+	# 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/"
+}
+
+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
+}
diff --git a/sci-biology/gbrowse/metadata.xml b/sci-biology/gbrowse/metadata.xml
index 3302123e5..2618ccd33 100644
--- a/sci-biology/gbrowse/metadata.xml
+++ b/sci-biology/gbrowse/metadata.xml
@@ -4,6 +4,10 @@
 	<maintainer>
 		<email>weaver@gentoo.org</email>
 		<name>Andrey Kislyuk</name>
+		<description>GBrowse is a generic genome browser.</description>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<longdescription lang="en">
+		GBrowse is a generic genome browser written in perl, could run as CGI, under mod_perl. Something called Apache::Registry should make it faster. It uses mysql or postgres as the storage engine.
+    </longdescription>
 </pkgmetadata>