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

4 files changed, 145 insertions, 0 deletions

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>
+
+