[med-svn] r5174 - in trunk/packages/ensembl/ensembl/57/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Fri Aug 20 18:52:34 UTC 2010
Author: moeller
Date: 2010-08-20 18:52:26 +0000 (Fri, 20 Aug 2010)
New Revision: 5174
Added:
trunk/packages/ensembl/ensembl/57/debian/ensembl.docs
trunk/packages/ensembl/ensembl/57/debian/ensembl.links
trunk/packages/ensembl/ensembl/57/debian/ensembl_web_user_db.sql
trunk/packages/ensembl/ensembl/57/debian/init.d
trunk/packages/ensembl/ensembl/57/debian/patches/apache_mods.patch
trunk/packages/ensembl/ensembl/57/debian/patches/biodas_lite.patch
trunk/packages/ensembl/ensembl/57/debian/patches/defaults_ini.patch
trunk/packages/ensembl/ensembl/57/debian/patches/mart_ini.patch
trunk/packages/ensembl/ensembl/57/debian/patches/sessiondbconn.patch
trunk/packages/ensembl/ensembl/57/debian/patches/sitedefs_pm.patch
trunk/packages/ensembl/ensembl/57/debian/patches/species_list.patch
Removed:
trunk/packages/ensembl/ensembl/57/debian/init.d.ex
Modified:
trunk/packages/ensembl/ensembl/57/debian/copyright
trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
trunk/packages/ensembl/ensembl/57/debian/patches/series
trunk/packages/ensembl/ensembl/57/debian/postinst
trunk/packages/ensembl/ensembl/57/debian/rules
Log:
Patches and config changes to ensembl that will hopefully make it launch first time.
Modified: trunk/packages/ensembl/ensembl/57/debian/copyright
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/copyright 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/copyright 2010-08-20 18:52:26 UTC (rev 5174)
@@ -6,6 +6,10 @@
cvs://cvs.sanger.ac.uk
+and the user database schema came from:
+
+ ftp://ftp.ensembl.org/pub/release-57/mysql/ensembl_web_user_db/ensembl_web_user_db.sql.gz
+
Upstream Author(s):
<put author's name and email here>
Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs 2010-08-20 18:52:26 UTC (rev 5174)
@@ -1,2 +1,6 @@
usr/share/ensembl
usr/bin
+var/log/ensembl/logs
+var/cache/ensembl/img-cache
+var/tmp/ensembl/img-tmp
+var/tmp/ensembl/tmp
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.docs
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.docs (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.docs 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1 @@
+debian/ensembl_web_user_db.sql
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.links
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.links (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.links 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,4 @@
+usr/share/ensembl/logs var/log/ensembl/logs
+usr/share/ensembl/img-cache var/cache/ensembl/img-cache
+usr/share/ensembl/img-tmp var/tmp/ensembl/img-tmp
+usr/share/ensembl/tmp var/tmp/ensembl/tmp
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl_web_user_db.sql
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl_web_user_db.sql (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl_web_user_db.sql 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,153 @@
+CREATE TABLE `cache` (
+ `type` varchar(16) NOT NULL DEFAULT '',
+ `code` varchar(64) NOT NULL DEFAULT '',
+ `data` mediumblob NOT NULL,
+ UNIQUE KEY `type` (`type`,`code`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `group_member` (
+ `group_member_id` int(11) NOT NULL AUTO_INCREMENT,
+ `webgroup_id` int(11) NOT NULL DEFAULT '0',
+ `user_id` int(11) NOT NULL DEFAULT '0',
+ `level` enum('member','administrator','superuser') NOT NULL DEFAULT 'member',
+ `status` enum('active','inactive','pending','barred') NOT NULL DEFAULT 'active',
+ `member_status` enum('active','inactive','pending','barred') DEFAULT 'inactive',
+ `created_by` int(11) NOT NULL DEFAULT '0',
+ `modified_by` int(11) NOT NULL DEFAULT '0',
+ `created_at` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_at` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+ PRIMARY KEY (`group_member_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=342 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `group_record` (
+ `group_record_id` int(11) NOT NULL AUTO_INCREMENT,
+ `webgroup_id` int(11) NOT NULL DEFAULT '0',
+ `type` varchar(255) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_by` int(11) DEFAULT NULL,
+ `modified_by` int(11) DEFAULT NULL,
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`group_record_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=528 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `group_record_vega` (
+ `group_record_vega_id` int(11) NOT NULL AUTO_INCREMENT,
+ `webgroup_id` int(11) DEFAULT NULL,
+ `type` varchar(255) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_by` int(11) DEFAULT NULL,
+ `modified_by` int(11) DEFAULT NULL,
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`group_record_vega_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `session` (
+ `last_session_no` int(10) unsigned NOT NULL DEFAULT '0'
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `session_record` (
+ `session_record_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `session_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type` enum('script','das','tmp','url','upload','message','custom_page') DEFAULT 'url',
+ `code` varchar(64) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_at` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_at` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+ `valid_thru` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`session_record_id`),
+ UNIQUE KEY `session_id` (`session_id`,`code`,`type`),
+ KEY `code_type` (`type`,`code`)
+) ENGINE=InnoDB AUTO_INCREMENT=6830126 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `sessions` (
+ `id` varchar(32) NOT NULL DEFAULT '',
+ `a_session` mediumtext NOT NULL,
+ `modified_at` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+ PRIMARY KEY (`id`),
+ KEY `modified_at` (`modified_at`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `temp` (
+ `code` varchar(32) NOT NULL DEFAULT '',
+ `data` mediumblob NOT NULL,
+ `created_at` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+ PRIMARY KEY (`code`),
+ KEY `created_at` (`created_at`)
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+
+CREATE TABLE `test` (
+ `session_record_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `session_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `type` enum('script','das','tmp','url','upload','message','foo') DEFAULT 'url',
+ `code` varchar(64) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_at` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_at` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `valid_thru` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00'
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `type` (
+ `type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(64) NOT NULL DEFAULT '',
+ PRIMARY KEY (`type_id`),
+ UNIQUE KEY `code` (`code`)
+) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `user` (
+ `user_id` int(11) NOT NULL AUTO_INCREMENT,
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `email` varchar(255) NOT NULL DEFAULT '',
+ `salt` varchar(8) NOT NULL DEFAULT '',
+ `password` varchar(64) DEFAULT '',
+ `data` text,
+ `organisation` text,
+ `status` enum('active','pending','suspended') NOT NULL DEFAULT 'pending',
+ `created_by` int(11) DEFAULT NULL,
+ `modified_by` int(11) DEFAULT NULL,
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`user_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=100280 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `user_record` (
+ `user_record_id` int(11) NOT NULL AUTO_INCREMENT,
+ `user_id` int(11) NOT NULL DEFAULT '0',
+ `type` varchar(255) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_by` int(11) DEFAULT NULL,
+ `modified_by` int(11) DEFAULT NULL,
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`user_record_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=9939 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `user_record_vega` (
+ `user_record_vega_id` int(11) NOT NULL AUTO_INCREMENT,
+ `user_id` int(11) NOT NULL DEFAULT '0',
+ `type` varchar(255) NOT NULL DEFAULT '',
+ `data` text NOT NULL,
+ `created_by` int(11) DEFAULT NULL,
+ `modified_by` int(11) DEFAULT NULL,
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`user_record_vega_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=100 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `webgroup` (
+ `webgroup_id` int(11) NOT NULL AUTO_INCREMENT,
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `blurb` text NOT NULL,
+ `data` text NOT NULL,
+ `type` enum('open','restricted','private') NOT NULL DEFAULT 'open',
+ `status` enum('active','inactive') NOT NULL DEFAULT 'active',
+ `created_by` int(11) NOT NULL DEFAULT '0',
+ `modified_by` int(11) NOT NULL DEFAULT '0',
+ `created_at` datetime DEFAULT NULL,
+ `modified_at` datetime DEFAULT NULL,
+ PRIMARY KEY (`webgroup_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=144 DEFAULT CHARSET=latin1;
+
Added: trunk/packages/ensembl/ensembl/57/debian/init.d
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/init.d (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/init.d 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,15 @@
+#!/bin/sh
+### BEGIN INIT INFO
+# Provides: ensembl
+# Required-Start: $local_fs $remote_fs $network $syslog
+# Required-Stop: $local_fs $remote_fs $network $syslog
+# Default-Start: 2 3 4 5
+# Default-Stop: 0 1 6
+# X-Interactive: true
+# Short-Description: Start/stop apache2-ensembl web server
+### END INIT INFO
+
+set -e
+
+APACHE_CONFDIR=/usr/share/ensembl /etc/init.d/apache2 $*
+
Property changes on: trunk/packages/ensembl/ensembl/57/debian/init.d
___________________________________________________________________
Added: svn:executable
+ *
Deleted: trunk/packages/ensembl/ensembl/57/debian/init.d.ex
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/init.d.ex 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/init.d.ex 2010-08-20 18:52:26 UTC (rev 5174)
@@ -1,154 +0,0 @@
-#!/bin/sh
-### BEGIN INIT INFO
-# Provides: ensembl
-# Required-Start: $network $local_fs
-# Required-Stop:
-# Default-Start: 2 3 4 5
-# Default-Stop: 0 1 6
-# Short-Description: <Enter a short description of the sortware>
-# Description: <Enter a long description of the software>
-# <...>
-# <...>
-### END INIT INFO
-
-# Author: Richard Holland <holland at eaglegenomics.com>
-
-# PATH should only include /usr/* if it runs after the mountnfs.sh script
-PATH=/sbin:/usr/sbin:/bin:/usr/bin
-DESC=ensembl # Introduce a short description here
-NAME=ensembl # Introduce the short server's name here
-DAEMON=/usr/sbin/ensembl # Introduce the server's location here
-DAEMON_ARGS="" # Arguments to run the daemon with
-PIDFILE=/var/run/$NAME.pid
-SCRIPTNAME=/etc/init.d/$NAME
-
-# Exit if the package is not installed
-[ -x $DAEMON ] || exit 0
-
-# Read configuration variable file if it is present
-[ -r /etc/default/$NAME ] && . /etc/default/$NAME
-
-# Load the VERBOSE setting and other rcS variables
-. /lib/init/vars.sh
-
-# Define LSB log_* functions.
-# Depend on lsb-base (>= 3.0-6) to ensure that this file is present.
-. /lib/lsb/init-functions
-
-#
-# Function that starts the daemon/service
-#
-do_start()
-{
- # Return
- # 0 if daemon has been started
- # 1 if daemon was already running
- # 2 if daemon could not be started
- start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON --test > /dev/null \
- || return 1
- start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON -- \
- $DAEMON_ARGS \
- || return 2
- # Add code here, if necessary, that waits for the process to be ready
- # to handle requests from services started subsequently which depend
- # on this one. As a last resort, sleep for some time.
-}
-
-#
-# Function that stops the daemon/service
-#
-do_stop()
-{
- # Return
- # 0 if daemon has been stopped
- # 1 if daemon was already stopped
- # 2 if daemon could not be stopped
- # other if a failure occurred
- start-stop-daemon --stop --quiet --retry=TERM/30/KILL/5 --pidfile $PIDFILE --name $NAME
- RETVAL="$?"
- [ "$RETVAL" = 2 ] && return 2
- # Wait for children to finish too if this is a daemon that forks
- # and if the daemon is only ever run from this initscript.
- # If the above conditions are not satisfied then add some other code
- # that waits for the process to drop all resources that could be
- # needed by services started subsequently. A last resort is to
- # sleep for some time.
- start-stop-daemon --stop --quiet --oknodo --retry=0/30/KILL/5 --exec $DAEMON
- [ "$?" = 2 ] && return 2
- # Many daemons don't delete their pidfiles when they exit.
- rm -f $PIDFILE
- return "$RETVAL"
-}
-
-#
-# Function that sends a SIGHUP to the daemon/service
-#
-do_reload() {
- #
- # If the daemon can reload its configuration without
- # restarting (for example, when it is sent a SIGHUP),
- # then implement that here.
- #
- start-stop-daemon --stop --signal 1 --quiet --pidfile $PIDFILE --name $NAME
- return 0
-}
-
-case "$1" in
- start)
- [ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC " "$NAME"
- do_start
- case "$?" in
- 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
- 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
- esac
- ;;
- stop)
- [ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
- do_stop
- case "$?" in
- 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
- 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
- esac
- ;;
- status)
- status_of_proc "$DAEMON" "$NAME" && exit 0 || exit $?
- ;;
- #reload|force-reload)
- #
- # If do_reload() is not implemented then leave this commented out
- # and leave 'force-reload' as an alias for 'restart'.
- #
- #log_daemon_msg "Reloading $DESC" "$NAME"
- #do_reload
- #log_end_msg $?
- #;;
- restart|force-reload)
- #
- # If the "reload" option is implemented then remove the
- # 'force-reload' alias
- #
- log_daemon_msg "Restarting $DESC" "$NAME"
- do_stop
- case "$?" in
- 0|1)
- do_start
- case "$?" in
- 0) log_end_msg 0 ;;
- 1) log_end_msg 1 ;; # Old process is still running
- *) log_end_msg 1 ;; # Failed to start
- esac
- ;;
- *)
- # Failed to stop
- log_end_msg 1
- ;;
- esac
- ;;
- *)
- #echo "Usage: $SCRIPTNAME {start|stop|restart|reload|force-reload}" >&2
- echo "Usage: $SCRIPTNAME {start|stop|status|restart|force-reload}" >&2
- exit 3
- ;;
-esac
-
-:
Added: trunk/packages/ensembl/ensembl/57/debian/patches/apache_mods.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/apache_mods.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/apache_mods.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,25 @@
+Index: ensembl-57/conf/httpd.conf
+===================================================================
+--- ensembl-57.orig/conf/httpd.conf 2010-08-20 19:49:53.037579151 +0200
++++ ensembl-57/conf/httpd.conf 2010-08-20 19:53:32.678574718 +0200
+@@ -15,16 +15,16 @@
+ # Load the required apache modules (unless built-into httpd)
+ # The .so files can be built with apxs if missing
+ <IfModule !perl_module>
+-LoadModule perl_module modules/mod_perl.so
++LoadModule perl_module /usr/lib/apache2/modules/mod_perl.so
+ </IfModule>
+ <IfModule !deflate_module>
+-LoadModule deflate_module modules/mod_deflate.so
++LoadModule deflate_module /usr/lib/apache2/modules/mod_deflate.so
+ </IfModule>
+ <IfModule !headers_module>
+-LoadModule headers_module modules/mod_headers.so
++LoadModule headers_module /usr/lib/apache2/modules/mod_headers.so
+ </IfModule>
+ <IfModule !expires_module>
+-LoadModule expires_module modules/mod_expires.so
++LoadModule expires_module /usr/lib/apache2/modules/mod_expires.so
+ </IfModule>
+ #
+ ####
Added: trunk/packages/ensembl/ensembl/57/debian/patches/biodas_lite.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/biodas_lite.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/biodas_lite.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,15 @@
+Index: ensembl-57/modules/Bio/Das/Lite.pm
+===================================================================
+--- ensembl-57.orig/modules/Bio/Das/Lite.pm 2010-08-20 20:11:36.249572927 +0200
++++ ensembl-57/modules/Bio/Das/Lite.pm 2010-08-20 20:12:23.722574652 +0200
+@@ -804,7 +804,9 @@
+
+ if (!$self->{'ua'}) {
+ $self->{'ua'} = Bio::Das::Lite::UserAgent->new();
+- $self->{'ua'}->proxy( ['http','https'], $self->http_proxy() );
++ if ($self->http_proxy()) {
++ $self->{'ua'}->proxy( ['http','https'], $self->http_proxy() );
++ }
+ $self->{'ua'}->no_proxy( @{ $self->no_proxy() } );
+ }
+
Added: trunk/packages/ensembl/ensembl/57/debian/patches/defaults_ini.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/defaults_ini.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/defaults_ini.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,66 @@
+Index: ensembl-57/public-plugins/mirror/conf/ini-files/DEFAULTS.ini
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ ensembl-57/public-plugins/mirror/conf/ini-files/DEFAULTS.ini 2010-08-20 20:10:35.874669268 +0200
+@@ -0,0 +1,61 @@
++[general]
++DATABASE_HOST = ensembldb.ensembl.org
++DATABASE_HOST_PORT = 5306
++DATABASE_WRITE_USER = anonymous
++DATABASE_WRITE_PASS =
++DATABASE_DBUSER = anonymous
++DATABASE_DBPASS =
++
++; ENSEMBL_WWW_PROXY = http://my_webcache.my_domain.org:3128
++
++[ENSEMBL_STYLE]
++; name of font used for labels...
++GRAPHIC_FONT = arial ; For true type fonts
++; GRAPHIC_FONT = small ; If true type fonts not installed
++
++; name of font used for DNA/Peptide sequence in boxes...
++GRAPHIC_FONT_FIXED = cour ; If using true type fonts
++; GRAPHIC_FONT_FIXED = Small ; If true type fonts not installed
++
++; path to ttfonts remember /
++GRAPHIC_TTF_PATH = /usr/share/fonts/truetype/msttcorefonts/ ; Install from corefonts.sourceforge.net
++; Default font-size for graphic text... (may need to change depending on fonts used above)
++; GRAPHIC_FONTSIZE = 8
++
++[ENSEMBL_INTERNAL_DAS_SOURCES]
++UniProt = 1
++Superfam = 1
++Phenotypes = 1
++
++[UniProt]
++dsn = aristotle
++description = Protein knowledgebase
++url = http://www.ebi.ac.uk/das-srv/uniprot/das
++type = uniprot/swissprot_acc
++authority = http://www.uniprot.org
++on = [ geneview protview ]
++col = orchid4
++
++[Superfam]
++dsn = to
++description = HMM library and genome assignments
++url = http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/das
++type = ensembl_peptide
++authority = http://supfam.mrc-lmb.cam.ac.uk/
++on = [ protview ]
++col = orchid1
++
++[Phenotypes]
++dsn = phenotypes
++description = Associated directly or via orthologues or protein families
++url = http://www.ebi.ac.uk/das-srv/genedas/das
++type = ensembl_gene
++authority =
++on = [ geneview ]
++col =
++
++[ENSEMBL_DICTIONARY]
++
++[ENSEMBL_BLAST_METHODS]
++dummy = 1;
++
Added: trunk/packages/ensembl/ensembl/57/debian/patches/mart_ini.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/mart_ini.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/mart_ini.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,13 @@
+Index: ensembl-57/public-plugins/mart/conf/SiteDefs.pm
+===================================================================
+--- ensembl-57.orig/public-plugins/mart/conf/SiteDefs.pm 2010-08-20 20:11:03.137535929 +0200
++++ ensembl-57/public-plugins/mart/conf/SiteDefs.pm 2010-08-20 20:11:09.173525817 +0200
+@@ -2,7 +2,7 @@
+
+ package EnsEMBL::Mart::SiteDefs;
+ sub update_conf {
+- $SiteDefs::ENSEMBL_MART_ENABLED = 1;
++ $SiteDefs::ENSEMBL_MART_ENABLED = 0;
+ }
+
+ 1;
Modified: trunk/packages/ensembl/ensembl/57/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-20 18:52:26 UTC (rev 5174)
@@ -1,2 +1,9 @@
debian-changes-57-1
calc_genotypes_config.patch
+apache_mods.patch
+species_list.patch
+sitedefs_pm.patch
+defaults_ini.patch
+mart_ini.patch
+biodas_lite.patch
+sessiondbconn.patch
Added: trunk/packages/ensembl/ensembl/57/debian/patches/sessiondbconn.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/sessiondbconn.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/sessiondbconn.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,15 @@
+Index: ensembl-57/modules/EnsEMBL/Web/DBSQL/SessionDBConnection.pm
+===================================================================
+--- ensembl-57.orig/modules/EnsEMBL/Web/DBSQL/SessionDBConnection.pm 2010-08-20 20:13:01.145520811 +0200
++++ ensembl-57/modules/EnsEMBL/Web/DBSQL/SessionDBConnection.pm 2010-08-20 20:13:32.881526913 +0200
+@@ -18,8 +18,8 @@
+ );
+ $caller->connection(
+ $dsn,
+- $species_defs->DATABASE_WRITE_USER,
+- $species_defs->DATABASE_WRITE_PASS,
++ $species_defs->ENSEMBL_USERDB_USER,
++ $species_defs->ENSEMBL_USERDB_PASS,
+ {
+ RaiseError => 1,
+ PrintError => 1,
Added: trunk/packages/ensembl/ensembl/57/debian/patches/sitedefs_pm.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/sitedefs_pm.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/sitedefs_pm.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,36 @@
+Index: ensembl-57/public-plugins/mirror/conf/SiteDefs.pm
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ ensembl-57/public-plugins/mirror/conf/SiteDefs.pm 2010-08-20 20:07:43.733562790 +0200
+@@ -0,0 +1,31 @@
++package EnsEMBL::Mirror::SiteDefs;
++use strict;
++
++sub update_conf {
++$SiteDefs::ENSEMBL_PORT = 8000;
++$SiteDefs::ENSEMBL_USER = 'nobody';
++$SiteDefs::ENSEMBL_GROUP = 'nogroup';
++
++# $SiteDefs::ENSEMBL_SERVERADMIN = 'my_user at my_domain.org';
++# $SiteDefs::ENSEMBL_SERVERNAME = 'my_ensembl.my_domain.org';
++# $SiteDefs::ENSEMBL_MAIL_SERVER = 'smtp.my_domain.org';
++# $SiteDefs::ENSEMBL_MAIL_COMMAND = '/usr/bin/Mail -s';
++# $SiteDefs::ENSEMBL_MAIL_ERRORS = 1;
++# $SiteDefs::ENSEMBL_ERRORS_TO = 'my_user at my_domain.org';
++
++# $SiteDefs::ENSEMBL_DEBUG_FLAGS = 24;
++# $SiteDefs::ENSEMBL_LONGPROCESS_MINTIME = 10;
++
++# $SiteDefs::ENSEMBL_TMP_DIR_BLAST = $SiteDefs::ENSEMBL_SERVERROOT."/blastqueue";
++# $SiteDefs::ENSEMBL_BLASTSCRIPT = $SiteDefs::ENSEMBL_SERVERROOT."/utils/runblast.pl";
++
++# $SiteDefs::ENSEMBL_USERDB_NAME = 'ensembl_web_user_db';
++# $SiteDefs::ENSEMBL_USERDB_USER = 'ensembl';
++# $SiteDefs::ENSEMBL_USERDB_HOST = 'localhost';
++# $SiteDefs::ENSEMBL_USERDB_PORT = 3306;
++# $SiteDefs::ENSEMBL_USERDB_PASS = 'ensembl';
++
++$SiteDefs::ENSEMBL_LOGINS = 0; ## Change to 1 to turn user logins on
++}
++
++1;
Added: trunk/packages/ensembl/ensembl/57/debian/patches/species_list.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/species_list.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/species_list.patch 2010-08-20 18:52:26 UTC (rev 5174)
@@ -0,0 +1,14 @@
+Index: ensembl-57/public-plugins/mirror/htdocs/info/about/species.html
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ ensembl-57/public-plugins/mirror/htdocs/info/about/species.html 2010-08-20 19:56:00.602575811 +0200
+@@ -0,0 +1,9 @@
++<html>
++<head>
++<title>Species List</title>
++</head>
++<body>
++<h1>Find a Species</h1>
++[[SCRIPT::EnsEMBL::Web::Document::HTML::SpeciesPage]]
++</body>
++</html>
Modified: trunk/packages/ensembl/ensembl/57/debian/postinst
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-20 18:52:26 UTC (rev 5174)
@@ -20,10 +20,17 @@
case "$1" in
configure)
- a2enmod perl
- a2enmod deflate
- a2enmod expires
- a2enmod headers
+ #a2enmod perl
+ #a2enmod deflate
+ #a2enmod expires
+ #a2enmod headers
+ mysql -uroot << EOMYSQL
+drop database if exists ensembl_web_user_db;
+create database ensembl_web_user_db;
+grant all privileges on ensembl_web_user_db.* to ensembl@'%' identified by 'ensembl';
+grant all privileges on ensembl_web_user_db.* to ensembl at localhost identified by 'ensembl';
+EOMYSQL
+ zcat /usr/share/doc/ensembl_web_user_db.sql.gz | mysql -uensembl -pensembl ensembl_web_user_db
;;
abort-upgrade|abort-remove|abort-deconfigure)
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 14:51:10 UTC (rev 5173)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-20 18:52:26 UTC (rev 5174)
@@ -35,7 +35,7 @@
ensembl-functgenomics ensembl-variation \
htdocs modules perl public-plugins utils \
$$d
- mv ensembl-variation/C_code/calc_genotypes $(CURDIR)/debian/ensembl/usr/bin/
+ mv ensembl-variation/C_code/calc_genotypes $(CURDIR)/debian/ensembl/usr/bin/
touch $@
install-paths: install-copying
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