[med-svn] r5188 - in trunk/packages/ensembl/ensembl/57/debian: . ensembl.overwrites patches
Steffen Möller
moeller at alioth.debian.org
Thu Aug 26 22:00:36 UTC 2010
Author: moeller
Date: 2010-08-26 22:00:33 +0000 (Thu, 26 Aug 2010)
New Revision: 5188
Added:
trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/
trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/Plugins.pm-dist
trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/README
trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/confSiteDefs.pm
trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/pluginSiteDefs.pm
trunk/packages/ensembl/ensembl/57/debian/patches/MULTI.ini.notforrelease57.patch
trunk/packages/ensembl/ensembl/57/debian/patches/SiteDefs_ENSEMBL_BLOCK.patch
trunk/packages/ensembl/ensembl/57/debian/patches/httpd.patch
Modified:
trunk/packages/ensembl/ensembl/57/debian/init.d
trunk/packages/ensembl/ensembl/57/debian/patches/series
trunk/packages/ensembl/ensembl/57/debian/postinst
trunk/packages/ensembl/ensembl/57/debian/rules
Log:
Roud of updates by Richard ... might actually work now :)
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/Plugins.pm-dist
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/Plugins.pm-dist (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/Plugins.pm-dist 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,11 @@
+## If you wish to use the EnsEMBL web-code from the command line, you will
+## need to hardcode the server root here
+
+## $SiteDefs::ENSEMBL_SERVERROOT = '/path to root of ensembl tree';
+
+$SiteDefs::ENSEMBL_PLUGINS = [
+ 'EnsEMBL::Mirror' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/mirror',
+ 'EnsEMBL::Ensembl' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/ensembl'
+];
+
+1;
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/README
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/README (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/README 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,4 @@
+The files in this folder will be used to directly overwrite
+similar files after all the install commands have been executed
+in debian/rules. This allows for an easier back-and-forth
+between the Debian package and the default configuration.
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/confSiteDefs.pm
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/confSiteDefs.pm (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/confSiteDefs.pm 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,1043 @@
+#!/usr/bin/perl -w
+###############################################################################
+#
+# Name: SiteDefs.pm
+#
+# Description: Localisation config for Ensembl website.
+#
+###############################################################################
+
+package SiteDefs;
+use strict;
+use Text::Wrap;
+use Config;
+$Text::Wrap::columns = 75;
+
+use vars qw ( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION
+ $APACHE_DIR
+ $APACHE_BIN
+ $BIOPERL_DIR
+ $CGI_POST_MAX
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ $ENSEMBL_VERSION
+ $ENSEMBL_PLUGINS $ENSEMBL_PLUGIN_ROOTS
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_SERVER
+ $ENSEMBL_PORT
+ $ENSEMBL_PROXY_PORT
+ $ENSEMBL_USER
+ $ENSEMBL_GROUP
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME $ENSEMBL_PROTOCOL
+ $ENSEMBL_MAIL_COMMAND
+ $ENSEMBL_MAIL_ERRORS
+ $ENSEMBL_ERRORS_TO
+ $ENSEMBL_LOGDIR
+ $ENSEMBL_PIDFILE
+ $ENSEMBL_ERRORLOG
+ $ENSEMBL_CUSTOMLOG
+ $ENSEMBL_NGINX_PIDFILE
+ $ENSEMBL_NGINX_ERRORLOG
+ $ENSEMBL_TEMPLATE_ROOT
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_TMP
+ $ENSEMBL_TMP_URL
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_DIR_DOTTER
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_TMP_DIR_CACHE
+ $ENSEMBL_TMP_URL_CACHE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_DATASETS
+ $ENSEMBL_SPECIES
+ $ENSEMBL_PRIMARY_SPECIES
+ $ENSEMBL_SECONDARY_SPECIES
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_SPECIES_ALIASES
+ $ENSEMBL_ENCRYPT_0
+ $ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ENCRYPT_2
+ $ENSEMBL_ENCRYPT_3
+ $ENSEMBL_USERDB_TYPE
+ $ENSEMBL_USERDB_PORT
+ $ENSEMBL_USERDB_NAME
+ $ENSEMBL_USERDB_HOST
+ $ENSEMBL_USERDB_USER
+ $ENSEMBL_USERDB_PASS
+ $ENSEMBL_COOKIEHOST
+ $ENSEMBL_USER_COOKIE
+ $ENSEMBL_USER_ID
+ $ENSEMBL_USERADMIN_ID
+ $ENSEMBL_WEBADMIN_ID
+ $ENSEMBL_LOGINS
+ $ENSEMBL_USER_DATA_TABLE
+ $ENSEMBL_GROUP_DATA_TABLE
+ $ENSEMBL_SESSION_COOKIE
+ $ENSEMBL_CONFIG_FILENAME
+ $ENSEMBL_CONFIG_BUILD
+ $ENSEMBL_HAS_C_EXTENSIONS
+ $ENSEMBL_LONGPROCESS_MINTIME
+ $ENSEMBL_APACHE_RELOAD
+ $ENSEMBL_SITETYPE
+ $ARCHIVE_VERSION
+ $BIOMART_URL
+ $MART_HELP_DESK
+ %OBJECT_TO_SCRIPT
+ %ENSEMBL_SETENV
+ @ENSEMBL_CONF_DIRS
+ @ENSEMBL_PERL_DIRS
+ @ENSEMBL_HTDOCS_DIRS
+ @ENSEMBL_LIB_DIRS
+ $ENSEMBL_SHORTEST_ALIAS
+ $MART_ENSEMBL_LINKS
+ $ENSEMBL_MART_ENABLED
+ $ENSEMBL_BLAST_ENABLED
+ $ENSEMBL_FLAG_NAMES
+);
+
+use Sys::Hostname::Long;
+use Exporter();
+ at ISA=qw(Exporter);
+
+$VERSION = 57;
+$ARCHIVE_VERSION = "Mar2010"; # Change this to the archive site for this version
+$ENSEMBL_RELEASE_DATE = 'Mar 2010';
+
+$ENSEMBL_MIN_SPARE_SERVERS = 5;
+$ENSEMBL_MAX_SPARE_SERVERS = 20;
+$ENSEMBL_START_SERVERS = 7;
+
+#### START OF VARIABLE DEFINITION #### DO NOT REMOVE OR CHANGE THIS COMMENT ####
+
+###############################################################################
+####################### LOCAL CONFIGURATION VARIABLES #########################
+###############################################################################
+
+##########################################################################
+# You need to change the following server root setting. It points to the
+# directory that contains htdocs, modules, perl, ensembl, etc
+# DO NOT LEAVE A TRAILING '/' ON ENSEMBL_SERVERROOT
+##########################################################################
+use File::Spec;
+
+my( $volume, $dir, $file ) = File::Spec->splitpath( __FILE__ );
+my @dir = File::Spec->splitdir( $dir );
+my @clean_directory = ();
+my $current_directory = File::Spec->curdir();
+my $parent_directory = File::Spec->updir();
+foreach( @dir ) {
+ next if $_ eq $current_directory; ## If we have a "." in the path ignore
+ if( $_ eq $parent_directory ) {
+ pop @clean_directory; ## If we have a ".." in the path remove the parent directory
+ } else {
+ push @clean_directory, $_; ## Otherwise add it!
+ }
+}
+
+#warn ".......... @clean_directory ..............";
+my $CONF_DIR = 'conf';
+while( ($CONF_DIR = pop @clean_directory) !~ /^conf/) { 1; } ## Remove up to the last "conf" directory...
+
+$ENSEMBL_SERVERROOT = File::Spec->catpath( $volume, File::Spec->catdir( @clean_directory ) );
+$ENSEMBL_SERVERROOT = '.' unless $ENSEMBL_SERVERROOT;
+$APACHE_DIR = "$ENSEMBL_SERVERROOT/apache2";
+
+$BIOPERL_DIR = "$ENSEMBL_SERVERROOT/bioperl-live";
+#warn "$ENSEMBL_SERVERROOT";
+## Define Plugin directories....
+eval qq(require '$ENSEMBL_SERVERROOT/$CONF_DIR/Plugins.pm');
+error( "Error requiring plugin file:\n$@" ) if $@;
+
+$CGI_POST_MAX = 5242880; # 5MB max upload
+
+$ENSEMBL_MART_ENABLED = 0;
+$ENSEMBL_BLAST_ENABLED = 0;
+
+$ENSEMBL_SERVER = Sys::Hostname::Long::hostname_long(); # Local machine name
+
+$ENSEMBL_PORT = 80;
+$ENSEMBL_PROXY_PORT = undef; # Port used for self-referential URLs:
+ # Set to undef if not using proxy-forwarding
+
+$ENSEMBL_SITETYPE = "Ensembl";
+$ENSEMBL_USER = getpwuid($>); # Auto-set web serveruser
+$ENSEMBL_GROUP = getgrgid($)); # Auto-set web server group
+
+$ENSEMBL_SERVERADMIN = 'webmaster@mydomain.org';
+$ENSEMBL_HELPDESK_EMAIL = $ENSEMBL_SERVERADMIN;
+$ENSEMBL_MAIL_SERVER = 'mail.mydomain.org';
+$ENSEMBL_SERVERNAME = 'www.mydomain.org';
+$ENSEMBL_PROTOCOL = 'http';
+$ENSEMBL_MAIL_COMMAND = '/usr/bin/Mail -s'; # Mail command
+$ENSEMBL_MAIL_ERRORS = '0'; # Do we want to email errors?
+$ENSEMBL_ERRORS_TO = 'webmaster@mydomain.org'; # ...and to whom?
+
+$ENSEMBL_API_VERBOSITY = 'WARNING';
+# 0 OFF NOTHING NONE
+# 1000 EXCEPTION THROW
+# 2000 (DEFAULT) WARNING WARN
+# 3000 DEPRECATE DEPRECATED
+# 4000 INFO
+# *1e6 ON ALL
+
+$ENSEMBL_DEBUG_FLAGS = 1;
+
+our $ENSEMBL_DEBUG_VERBOSE_ERRORS = 0;
+our $ENSEMBL_FLAG_NAMES_HR = [];
+
+$ENSEMBL_FLAG_NAMES = [qw(
+ GENERAL_ERRORS
+ DRAWING_CODE
+ SD_AUTOLOADER
+ HANDLER_ERRORS
+ LONG_PROCESS
+ PERL_PROFILER
+ TIMESTAMPED_LOGS
+ TREE_DUMPS
+ REFERER
+ MAGIC_MESSAGES
+ JAVASCRIPT_DEBUG
+ MEMCACHED
+ EXTERNAL_COMMANDS
+ WIZARD_MESSAGES
+ VERBOSE_STARTUP
+)];
+
+my $i=0;
+
+foreach( @$ENSEMBL_FLAG_NAMES ) {
+no strict 'refs';
+ my $variable_name = 'SiteDefs::ENSEMBL_DEBUG_'.$_;
+ $$variable_name = 1<<($i++);
+ $ENSEMBL_DEBUG_VERBOSE_ERRORS <<=1;
+ $ENSEMBL_DEBUG_VERBOSE_ERRORS +=1;
+ (my $t = ucfirst(lc($_)) ) =~ s/_/ /g;
+ push @{$ENSEMBL_FLAG_NAMES_HR}, $t;
+}
+
+#####################
+# Apache files
+$ENSEMBL_PIDFILE = undef;
+$ENSEMBL_ERRORLOG = undef;
+$ENSEMBL_CUSTOMLOG = undef;
+
+$ENSEMBL_TMPL_CSS = '/css/ensembl.css';
+$ENSEMBL_PAGE_CSS = '/css/content.css';
+$ENSEMBL_IMAGE_WIDTH = 800;
+#####################
+# TMP dirs
+# ENSEMBL_TMP_DIR points to a filesystem dir
+# ENSEMBL_TMP_URL points to a URL location.
+# httpd.conf creates an alias for ENSEMBL_TMP_URL to ENSEMBL_TMP_DIR
+# httpd.conf also validates the existence of ENSEMBL_TMP_DIR.
+
+$ENSEMBL_TMP_CREATE = 1; # Create tmp dirs on server startup if not found?
+$ENSEMBL_TMP_DELETE = 0; # Delete files from the tmp dir on server startup?
+$ENSEMBL_TMP_TMP = '/tmp';
+$ENSEMBL_TMP_URL = '/tmp';
+$ENSEMBL_TMP_URL_IMG = '/img-tmp';
+$ENSEMBL_TMP_URL_CACHE = '/img-cache';
+
+#$ENSEMBL_TMP_DIR_BLAST = '/ensemblweb/shared/data/blastqueue';
+#$ENSEMBL_TMP_DIR_BLAST_OLD = '/ensweb/shared/data/blastqueue';
+$ENSEMBL_BLASTSCRIPT = undef;
+$ENSEMBL_REGISTRY = undef;
+$ENSEMBL_PRIVATE_AUTH = undef;
+####################
+# Environment variables to set using the SetEnv directive
+%ENSEMBL_SETENV =
+ ( # --- LSF ---
+ LSF_BINDIR => $ENV{LSF_BINDIR} || '',
+ LSF_SERVERDIR => $ENV{LSF_SERVERDIR} || '',
+ LSF_LIBDIR => $ENV{LSF_LIBDIR} || '',
+ XLSF_UIDDIR => $ENV{XLSF_UIDDIR} || '',
+ LD_LIBRARY_PATH => $ENV{LD_LIBRARY_PATH} || '',
+ );
+
+####
+# Content dirs
+# @ENSEMBL_CONF_DIRS locates <species>.ini files
+# @ENSEMBL_PERL_DIRS locates mod-perl scripts
+# @ENSEMBL_HTDOCS_DIRS locates static content
+# @ENSEMBL_LIB_DIRS locates perl library modules.
+# Array order is maintained in @INC
+ at ENSEMBL_CONF_DIRS = ($ENSEMBL_SERVERROOT.'/'.$CONF_DIR);
+ at ENSEMBL_PERL_DIRS = (
+ $ENSEMBL_SERVERROOT.'/perl',
+);
+
+ at ENSEMBL_HTDOCS_DIRS = (
+ $ENSEMBL_SERVERROOT.'/htdocs',
+ $ENSEMBL_SERVERROOT.'/biomart-perl/htdocs'
+);
+
+###############################################################################
+######################### END OF LOCAL CONFIGURATION SECTION ##################
+###############################################################################
+
+###############################################################################
+## Choice of species...
+###############################################################################
+
+$ENSEMBL_PRIMARY_SPECIES = 'Homo_sapiens'; # Default species
+
+## This hash is used to configure the species available in this
+## copy of EnsEMBL - comment out any lines which are not relevant
+## If you add a new species MAKE sure that one of the values of the
+## array is the "SPECIES_CODE" defined in the species.ini file
+
+our %__species_aliases = ();
+
+###############################################################################
+## Web user datbase - used to store information about settings, e.g. DAS
+## contigview and cytoview options.
+###############################################################################
+
+$ENSEMBL_VERSION = $VERSION;
+$ENSEMBL_USERDB_TYPE = 'mysql';
+$ENSEMBL_USERDB_NAME = 'ensembl_web_user_db';
+$ENSEMBL_USERDB_USER = 'mysqluser';
+$ENSEMBL_USERDB_HOST = 'localhost';
+$ENSEMBL_USERDB_PORT = 3305;
+$ENSEMBL_USERDB_PASS = '';
+
+$ENSEMBL_USER_COOKIE = 'ENSEMBL_WWW_USER';
+$ENSEMBL_USER_ID = 0;
+$ENSEMBL_USERADMIN_ID = 0;
+$ENSEMBL_WEBADMIN_ID = 0;
+$ENSEMBL_LOGINS = 0;
+$ENSEMBL_USER_DATA_TABLE = 'user_record';
+$ENSEMBL_GROUP_DATA_TABLE = 'group_record';
+$ENSEMBL_SESSION_COOKIE = 'ENSEMBL_WWW_SESSION';
+$ENSEMBL_COOKIEHOST = ''; #.ensembl.org';
+
+$ENSEMBL_ENCRYPT_0 = 0x16a3b3; # Encryption keys for session
+$ENSEMBL_ENCRYPT_1 = 'a9'; # Encryption keys for session
+$ENSEMBL_ENCRYPT_2 = 'xX'; # Encryption keys for session
+$ENSEMBL_ENCRYPT_3 = '2Q'; # Encryption keys for session
+$ENSEMBL_ENCRYPT_EXPIRY = 60; # Cookies last 60 days
+$ENSEMBL_ENCRYPT_REFRESH = 30; # Refresh cookies with less than 30 days to go
+
+$ENSEMBL_MINIAD_DIR = $ENSEMBL_SERVERROOT.'/htdocs/img/mini-ads/';
+
+###############################################################################
+## General systems bumf
+###############################################################################
+
+$ENSEMBL_CONFIG_FILENAME = 'config.packed';
+$ENSEMBL_CONFIG_BUILD = 0; # Build config on server startup?
+ # Setting to 0 will try to recover from
+ # $ENSEMBL_CONFIG_FILENAME on startup
+$ENSEMBL_APACHE_RELOAD = 0; # Debug setting - set to 0 for release
+
+$ENSEMBL_HAS_C_EXTENSIONS = 1;
+$ENSEMBL_LONGPROCESS_MINTIME = 10;
+
+## ALLOWABLE DATA OBJECTS
+%OBJECT_TO_SCRIPT = (
+ Config => 'config',
+ Component => 'component',
+ Zmenu => 'zmenu',
+ Blast => 'blast',
+
+ Gene => 'action',
+ Transcript => 'action',
+ Location => 'action',
+ Variation => 'action',
+ Regulation => 'action',
+ Server => 'action',
+ Info => 'action',
+ Search => 'action',
+ UniSearch => 'action',
+ News => 'action',
+
+ Account => 'modal',
+ UserData => 'modal',
+ Help => 'modal',
+ Export => 'modal',
+);
+
+
+###############################################################################
+##
+## PLUGIN CODE.... We need to use the plugin modules
+##
+## First of all look in "Plugins.pm" to get the definitions...
+##
+###############################################################################
+
+sub tmp {
+ my $tmp_dir = shift;
+
+ $SiteDefs::ENSEMBL_TMP_DIR = $tmp_dir;
+ $SiteDefs::ENSEMBL_TMP_DIR_IMG = "$tmp_dir/img/tmp";
+ $SiteDefs::ENSEMBL_TMP_DIR_CACHE = "$tmp_dir/img/cache";
+ $SiteDefs::ENSEMBL_TMP_DIR_DOTTER = "$tmp_dir/dotter";
+ $SiteDefs::ENSEMBL_TMP_DIR_BLAST = "$tmp_dir/blastqueue";
+}
+
+sub logs {
+ my $log_dir = shift;
+ my $datestamp = '';
+ if( $SiteDefs::ENSEMBL_DEBUG_FLAGS & $SiteDefs::ENSEMBL_DEBUG_TIMESTAMPED_LOGS ) {
+ my @time = gmtime();
+ $datestamp = sprintf( ".%04d-%02d-%02d-%02d-%02d-%02d", $time[5]+1900, $time[4]+1, @time[3,2,1,0] );
+ }
+
+## Set all log files into the /ensemblweb/tmp/logs/uswest/ directory
+ my $log_prefix = "$log_dir/".$SiteDefs::ENSEMBL_SERVER;
+ $SiteDefs::ENSEMBL_LOGDIR = "$log_dir";
+ $SiteDefs::ENSEMBL_PIDFILE = "$log_prefix.httpd.pid";
+ $SiteDefs::ENSEMBL_ERRORLOG = "$log_prefix$datestamp.error_log";
+ $SiteDefs::ENSEMBL_CUSTOMLOG = "$log_prefix$datestamp.access_log ensembl_extended";
+}
+
+sub memcached {
+ my $pars = shift;
+ $pars->{'servers'} = [] unless exists $pars->{'servers'};
+ unless( @{$pars->{'servers'}} ) {
+ $SiteDefs::ENSEMBL_MEMCACHED = undef;
+ return;
+ }
+ $pars->{'debug'} = 0 unless exists $pars->{'debug'};
+ $pars->{'hm_stats'} = 0 unless exists $pars->{'hm_stats'};
+
+ my %flags = map { ( $_ => 1) } qw(
+ PLUGGABLE_PATHS
+ STATIC_PAGES_CONTENT
+ WEBSITE_DB_DATA
+ USER_DB_DATA
+ DYNAMIC_PAGES_CONTENT
+ TMP_IMAGES
+ ORDERED_TREE
+ OBJECTS_COUNTS
+ IMAGE_CONFIG
+ );
+ foreach my $k ( keys %{$pars->{'flags'}} ) {
+ if( $pars->{'flags'}{$k} ) {
+ $flags{ $k } = 1;
+ } else {
+ delete $flags{ $k };
+ }
+ }
+ $pars->{'flags'} = [ keys %flags ];
+
+ $SiteDefs::ENSEMBL_MEMCACHED = $pars;
+}
+
+=for Information
+
+Use flags to enable what you would like to cache:
+
+ * PLUGGABLE_PATHS - paths to pluggable scripts and static files
+ * STATIC_PAGES_CONTENT - .html pages content, any pages which SendDecPafe handler is responsible for
+ * WEBSITE_DB_DATA - website db data queries results
+ * USER_DB_DATA - user and group db data queries results (records, etc.)
+ * DYNAMIC_PAGES_CONTENT - all dynamic ajax responses
+ * TMP_IMAGES - temporary images (the one you see actual genomic data on) and their imagemaps
+ * ORDERED_TREE - navigation tree
+ * OBJECTS_COUNTS - defferent counts for objects like gene, transcript, location, etc...
+ * IMAGE_CONFIG - Image configurations
+
+=cut
+
+sub error {
+ my $message = join "\n", @_;
+ $message =~ s/\s+$//sm;
+ warn "#" x 78, "\n",
+ wrap("# ","# ", $message ),
+ "\n", "#" x 78, "\n";
+}
+
+logs("$ENSEMBL_SERVERROOT/logs");
+tmp( "$ENSEMBL_SERVERROOT/tmp" );
+
+my @T = reverse @{$ENSEMBL_PLUGINS||[]};
+while( my( $dir, $name ) = splice(@T,0,2) ) {
+ my $plugin_conf = $name."::SiteDefs";
+ eval "require '$dir/conf/SiteDefs.pm'";
+ if($@) {
+ my $message = "Can't locate $dir/conf/SiteDefs.pm in";
+ error( "Error requiring $plugin_conf:\n$@" ) unless $@ =~ m:$message:;
+ } else {
+ my $FN = $plugin_conf.'::update_conf';
+ eval "$FN()";
+ if( $@ ) {
+ my $message = "Undefined subroutine &$FN called at ";
+ if( $@ =~ /$message/ ) {
+ error( "Function $FN not defined in $dir/conf/SiteDefs.pm" );
+ } else {
+ error( "Error calling $FN in $dir/conf/SiteDefs.pm\n$@" );
+ }
+ }
+ }
+}
+
+$APACHE_BIN ||= "$APACHE_DIR/bin/httpd";
+
+#### END OF VARIABLE DEFINITION #### DO NOT REMOVE OR CHANGE THIS COMMENT ####
+###############################################################################
+# You should not change anything below here
+###############################################################################
+
+ at ENSEMBL_LIB_DIRS = (
+ $APACHE_DIR."lib/perl5/site_perl/$Config{'version'}/$Config{archname}/",
+ $ENSEMBL_SERVERROOT.'/ensembl/modules',
+ $ENSEMBL_SERVERROOT.'/ensembl-compara/modules',
+ $ENSEMBL_SERVERROOT.'/ensembl-draw/modules',
+ $ENSEMBL_SERVERROOT.'/ensembl-variation/modules',
+ $ENSEMBL_SERVERROOT.'/ensembl-functgenomics/modules',
+ $ENSEMBL_SERVERROOT.'/ensembl-external/modules',
+ $ENSEMBL_SERVERROOT.'/biomart-perl/lib',
+ $BIOPERL_DIR,
+ $ENSEMBL_SERVERROOT.'/modules',
+);
+
+ at T = reverse @{$ENSEMBL_PLUGINS||[]}; ## These have to go on in reverse order...
+$ENSEMBL_PLUGIN_ROOTS = ();
+while( my( $dir, $name ) = splice(@T,0,2) ) {
+ unshift @ENSEMBL_PERL_DIRS, $dir.'/perl';
+ unshift @ENSEMBL_HTDOCS_DIRS, $dir.'/htdocs';
+ unshift @$ENSEMBL_PLUGIN_ROOTS, $name;
+ push @ENSEMBL_CONF_DIRS, $dir.'/conf';
+ unshift @ENSEMBL_LIB_DIRS, $dir.'/modules';
+}
+
+ at T = @{$ENSEMBL_PLUGINS||[]}; ## But these have to go on in normal order...
+while( my( $name, $dir ) = splice(@T,0,2) ) {
+}
+
+ at ENSEMBL_LIB_DIRS = reverse @ENSEMBL_LIB_DIRS; # Helps getting @inc into
+ # right order
+
+$ENSEMBL_PROXY_PORT = $ENSEMBL_PORT unless ( $ENSEMBL_PROXY_PORT && $ENSEMBL_PROXY_PORT ne "" );
+
+#-# Autogeneration stuff.... DO NOT TOUCH THIS - it does nasty stuff....
+
+## Add self refernetial elements to ENSEMBL_SPECIES_ALIASES
+## And one without the _ in...
+
+$ENSEMBL_SPECIES_ALIASES = {};
+$ENSEMBL_DATASETS = [ sort keys %__species_aliases ];
+
+foreach my $name ( @$ENSEMBL_DATASETS ) {
+ foreach my $alias ( @{$__species_aliases{$name}} ) {
+ $ENSEMBL_SPECIES_ALIASES->{lc($alias)} = $name;
+ }
+ my $key = lc($name);
+ $ENSEMBL_SPECIES_ALIASES->{$key} = $name; # homo_sapiens
+ $key =~s/\.//g;
+ $ENSEMBL_SPECIES_ALIASES->{$key} = $name; # homosapiens
+ $key = lc($name);
+ $key =~s/^([a-z])[a-z]*_/$1_/g;
+ $ENSEMBL_SPECIES_ALIASES->{$key} = $name; # h_sapiens
+ $key =~s/_/\./g;
+ $ENSEMBL_SPECIES_ALIASES->{$key} = $name; # h.sapiens
+ $key =~s/_//g;
+ $ENSEMBL_SPECIES_ALIASES->{$key} = $name; # hsapiens
+}
+$ENSEMBL_SHORTEST_ALIAS = {};
+foreach my $key (keys %$ENSEMBL_SPECIES_ALIASES) {
+ my $bin = $ENSEMBL_SPECIES_ALIASES->{$key};
+ $ENSEMBL_SHORTEST_ALIAS->{$bin} = $key if !exists($ENSEMBL_SHORTEST_ALIAS->{$bin}) ||
+ length($key) < length($ENSEMBL_SHORTEST_ALIAS->{$bin});
+
+}
+my @temp_species = @{$ENSEMBL_DATASETS};
+unless( $__species_aliases{$ENSEMBL_PRIMARY_SPECIES} ) {
+ error( qq(Species "$ENSEMBL_PRIMARY_SPECIES" not defined in ENSEMBL_SPECIES_ALIASES) );
+ $ENSEMBL_PRIMARY_SPECIES = shift @temp_species;
+}
+unless( $__species_aliases{$ENSEMBL_SECONDARY_SPECIES} ) {
+ error( qq(Species "$ENSEMBL_SECONDARY_SPECIES" not defined in ENSEMBL_SPECIES_ALIASES) );
+ $ENSEMBL_SECONDARY_SPECIES = shift @temp_species;
+}
+$ENSEMBL_SECONDARY_SPECIES = shift @temp_species if $ENSEMBL_SECONDARY_SPECIES eq $ENSEMBL_PRIMARY_SPECIES;
+
+$ENSEMBL_SERVERNAME ||= $ENSEMBL_SERVER;
+## here we try and do the dynamic use stuff;
+$BIOMART_URL = 'Multi';
+$ENSEMBL_BASE_URL = "$ENSEMBL_PROTOCOL://$ENSEMBL_SERVERNAME".
+ ( $ENSEMBL_PROXY_PORT==80 && $ENSEMBL_PROTOCOL eq 'http' ||
+ $ENSEMBL_PROXY_PORT==443 && $ENSEMBL_PROTOCOL eq 'https' ? '' : ":$ENSEMBL_PROXY_PORT" );
+
+$ENSEMBL_SITE_URL = $ENSEMBL_BASE_URL.'/';
+$ENSEMBL_SITE_URL .= $ENSEMBL_SITE_DIR.'/' if $ENSEMBL_SITE_DIR;
+
+$MART_ENSEMBL_LINKS = $ENSEMBL_BASE_URL;
+$MART_HELP_DESK = $ENSEMBL_SITE_URL.'default/helpview';
+$ENSEMBL_TEMPLATE_ROOT = $ENSEMBL_SERVERROOT.'/biomart-perl/conf';
+
+####################
+# Export by default
+####################
+ at EXPORT = qw(
+ $ENSEMBL_FLAG_NAMES
+ $APACHE_DIR
+ $BIOPERL_DIR
+ $CGI_POST_MAX
+ $ENSEMBL_PLUGIN_ROOTS
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_PLUGINS
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_SERVER
+ $ENSEMBL_PORT
+ $ENSEMBL_PROXY_PORT
+ $ENSEMBL_USER
+ $ENSEMBL_GROUP
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME $ENSEMBL_PROTOCOL
+ $ENSEMBL_MAIL_COMMAND
+ $ENSEMBL_MAIL_ERRORS
+ $ENSEMBL_ERRORS_TO
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR_DOTTER
+ $ENSEMBL_TMP_TMP
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_URL
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_TMP_DIR_CACHE
+ $ENSEMBL_TMP_URL_CACHE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_DATASETS
+ $ENSEMBL_SPECIES
+ $ENSEMBL_CONFIG_FILENAME
+ $ENSEMBL_CONFIG_BUILD
+ $ENSEMBL_HAS_C_EXTENSIONS
+ $ENSEMBL_VERSION
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ $ENSEMBL_SHORTEST_ALIAS
+ $MART_ENSEMBL_LINKS
+);
+
+############################
+# Export anything asked for
+############################
+ at EXPORT_OK = qw(
+ $ENSEMBL_FLAG_NAMES
+ $APACHE_DIR
+ $CGI_POST_MAX
+ $BIOPERL_DIR
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ $ENSEMBL_VERSION
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_PLUGIN_ROOTS
+ %ENSEMBL_SETENV
+ @ENSEMBL_CONF_DIRS
+ @ENSEMBL_PERL_DIRS
+ @ENSEMBL_HTDOCS_DIRS
+ @ENSEMBL_LIB_DIRS
+ $ENSEMBL_SHORTEST_ALIAS
+
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_PLUGINS
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_SERVER
+ $ENSEMBL_PORT
+ $ENSEMBL_PROXY_PORT
+ $ENSEMBL_USER
+ $ENSEMBL_GROUP
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME $ENSEMBL_PROTOCOL
+ $ENSEMBL_MAIL_COMMAND
+ $ENSEMBL_MAIL_ERRORS
+ $ENSEMBL_ERRORS_TO
+ $ENSEMBL_LOGDIR
+ $ENSEMBL_PIDFILE
+ $ENSEMBL_ERRORLOG
+ $ENSEMBL_CUSTOMLOG
+ $ENSEMBL_NGINX_PIDFILE
+ $ENSEMBL_NGINX_ERRORLOG
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_TMP
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR_DOTTER
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_URL
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_TMP_DIR_CACHE
+ $ENSEMBL_TMP_URL_CACHE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_DATASETS
+ $ENSEMBL_SPECIES
+ $ENSEMBL_PRIMARY_SPECIES
+ $ENSEMBL_SECONDARY_SPECIES
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_SPECIES_ALIASES
+ $ENSEMBL_ENCRYPT_0
+ $ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ENCRYPT_2
+ $ENSEMBL_ENCRYPT_3
+ $ENSEMBL_USERDB_TYPE
+ $ENSEMBL_USERDB_PORT
+ $ENSEMBL_USERDB_NAME
+ $ENSEMBL_USERDB_HOST
+ $ENSEMBL_USERDB_USER
+ $ENSEMBL_USERDB_PASS
+ $ENSEMBL_COOKIEHOST
+ $ENSEMBL_USER_COOKIE
+ $ENSEMBL_USER_ID
+ $ENSEMBL_USERADMIN_ID
+ $ENSEMBL_WEBADMIN_ID
+ $ENSEMBL_LOGINS
+ $ENSEMBL_USER_DATA_TABLE
+ $ENSEMBL_GROUP_DATA_TABLE
+ $ENSEMBL_SESSION_COOKIE
+ $ENSEMBL_CONFIG_FILENAME
+ $ENSEMBL_CONFIG_BUILD
+ $ENSEMBL_HAS_C_EXTENSIONS
+ $ENSEMBL_LONGPROCESS_MINTIME
+ $ENSEMBL_APACHE_RELOAD
+ $ENSEMBL_SITETYPE
+ $ARCHIVE_VERSION
+ $MART_ENSEMBL_LINKS
+ $ENSEMBL_MART_ENABLED
+ $ENSEMBL_BLAST_ENABLED
+);
+
+###################################
+# Export groups asked for by name
+###################################
+%EXPORT_TAGS = (
+ ALL => [qw(
+ $ENSEMBL_FLAG_NAMES
+ $APACHE_DIR
+ $CGI_POST_MAX
+ $BIOPERL_DIR
+ $ENSEMBL_SHORTEST_ALIAS
+ $ENSEMBL_PLUGINS $ENSEMBL_PLUGIN_ROOTS
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_SERVER
+ $ENSEMBL_PORT
+ $ENSEMBL_PROXY_PORT
+ $ENSEMBL_USER
+ $ENSEMBL_GROUP
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME $ENSEMBL_PROTOCOL
+ $ENSEMBL_MAIL_COMMAND
+ $ENSEMBL_MAIL_ERRORS
+ $ENSEMBL_ERRORS_TO
+ $ENSEMBL_LOGDIR
+ $ENSEMBL_PIDFILE
+ $ENSEMBL_ERRORLOG
+ $ENSEMBL_CUSTOMLOG
+ $ENSEMBL_NGINX_PIDFILE
+ $ENSEMBL_NGINX_ERRORLOG
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR_DOTTER
+ $ENSEMBL_TMP_TMP
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_URL
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_TMP_DIR_CACHE
+ $ENSEMBL_TMP_URL_CACHE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_DATASETS
+ $ENSEMBL_SPECIES
+ $ENSEMBL_PRIMARY_SPECIES
+ $ENSEMBL_SECONDARY_SPECIES
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_SPECIES_ALIASES
+ $ENSEMBL_ENCRYPT_0
+ $ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ENCRYPT_2
+ $ENSEMBL_ENCRYPT_3
+ $ENSEMBL_USERDB_TYPE
+ $ENSEMBL_USERDB_PORT
+ $ENSEMBL_USERDB_NAME
+ $ENSEMBL_USERDB_HOST
+ $ENSEMBL_USERDB_USER
+ $ENSEMBL_USERDB_PASS
+ $ENSEMBL_COOKIEHOST
+ $ENSEMBL_USER_COOKIE
+ $ENSEMBL_USER_ID
+ $ENSEMBL_USERADMIN_ID
+ $ENSEMBL_WEBADMIN_ID
+ $ENSEMBL_LOGINS
+ $ENSEMBL_USER_DATA_TABLE
+ $ENSEMBL_GROUP_DATA_TABLE
+ $ENSEMBL_SESSION_COOKIE
+ $ENSEMBL_CONFIG_FILENAME
+ $ENSEMBL_CONFIG_BUILD
+ $ENSEMBL_LONGPROCESS_MINTIME
+ $ENSEMBL_HAS_C_EXTENSIONS
+ $ENSEMBL_APACHE_RELOAD
+ $ENSEMBL_SITETYPE
+ $ARCHIVE_VERSION
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_VERSION
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ %ENSEMBL_SETENV
+ @ENSEMBL_CONF_DIRS
+ @ENSEMBL_PERL_DIRS
+ @ENSEMBL_HTDOCS_DIRS
+ @ENSEMBL_LIB_DIRS
+ $MART_ENSEMBL_LINKS
+ $ENSEMBL_MART_ENABLED
+ $ENSEMBL_BLAST_ENABLED
+ )],
+
+ WEB => [qw(
+ $ENSEMBL_FLAG_NAMES
+ $APACHE_DIR
+ $CGI_POST_MAX
+ $BIOPERL_DIR
+ $ENSEMBL_PLUGIN_ROOTS
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ $ENSEMBL_VERSION
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_PLUGINS
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR_DOTTER
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_TMP
+ $ENSEMBL_TMP_DIR
+ $ENSEMBL_TMP_URL
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_TMP_DIR_CACHE
+ $ENSEMBL_TMP_URL_CACHE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_SERVER
+ $ENSEMBL_PORT
+ $ENSEMBL_PROXY_PORT
+ $ENSEMBL_USER
+ $ENSEMBL_GROUP
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME $ENSEMBL_PROTOCOL
+ $ENSEMBL_MAIL_COMMAND
+ $ENSEMBL_MAIL_ERRORS
+ $ENSEMBL_ERRORS_TO
+ $ENSEMBL_LOGDIR
+ $ENSEMBL_PIDFILE
+ $ENSEMBL_ERRORLOG
+ $ENSEMBL_CUSTOMLOG
+ $ENSEMBL_NGINX_PIDFILE
+ $ENSEMBL_NGINX_ERRORLOG
+ $ENSEMBL_HAS_C_EXTENSIONS
+ $ENSEMBL_APACHE_RELOAD
+ %ENSEMBL_SETENV
+ @ENSEMBL_HTDOCS_DIRS
+ $ENSEMBL_SHORTEST_ALIAS
+ @ENSEMBL_LIB_DIRS
+ @ENSEMBL_PERL_DIRS
+ $MART_ENSEMBL_LINKS
+ $ENSEMBL_MART_ENABLED
+ $ENSEMBL_BLAST_ENABLED
+ )],
+
+ APACHE => [qw(
+ $ENSEMBL_FLAG_NAMES
+ $APACHE_DIR
+ $CGI_POST_MAX
+ $BIOPERL_DIR
+ $ENSEMBL_PLUGIN_ROOTS
+ $ENSEMBL_HELPDESK_EMAIL
+ $ENSEMBL_MAIL_SERVER
+ $ENSEMBL_VERSION
+ $ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
+ $ENSEMBL_TMPL_CSS
+ $ENSEMBL_PAGE_CSS
+ $ENSEMBL_IMAGE_WIDTH
+ $ENSEMBL_PLUGINS
+ $ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
+ $ENSEMBL_API_VERBOSITY $ENSEMBL_DEBUG_FLAGS
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_BLASTSCRIPT
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_BLAST_OLD
+ $ENSEMBL_DATASETS
+ $ENSEMBL_SPECIES
+ $ENSEMBL_PRIMARY_SPECIES
+ $ENSEMBL_SECONDARY_SPECIES
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_SPECIES_ALIASES
+ $ENSEMBL_ENCRYPT_0
+ $ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ENCRYPT_2
+ $ENSEMBL_ENCRYPT_3
+ $ENSEMBL_USERDB_TYPE
+ $ENSEMBL_USERDB_PORT
+ $ENSEMBL_USERDB_NAME
+ $ENSEMBL_USERDB_HOST
+ $ENSEMBL_USERDB_USER
+ $ENSEMBL_USERDB_PASS
+ $ENSEMBL_COOKIEHOST
+ $ENSEMBL_USER_COOKIE
+ $ENSEMBL_USER_ID
+ $ENSEMBL_USERADMIN_ID
+ $ENSEMBL_WEBADMIN_ID
+ $ENSEMBL_LOGINS
+ $ENSEMBL_USER_DATA_TABLE
+ $ENSEMBL_GROUP_DATA_TABLE
+ $ENSEMBL_SESSION_COOKIE
+ $ENSEMBL_MINIAD_DIR
+ $ENSEMBL_CONFIG_FILENAME
+ $ENSEMBL_CONFIG_BUILD
+ $ENSEMBL_LONGPROCESS_MINTIME
+ $ENSEMBL_SITETYPE
+ $ENSEMBL_SHORTEST_ALIAS
+ $ARCHIVE_VERSION
+ $MART_ENSEMBL_LINKS
+ $ENSEMBL_MART_ENABLED
+ $ENSEMBL_BLAST_ENABLED
+ )],
+);
+
+
+
+__END__
+
+=head1 NAME
+
+SiteDefs
+
+=head1 SYNOPSIS
+
+ use <path>::SiteDefs;
+ # Brief but working code example(s) here showing the most common usage
+
+ # This section will be as far as many users bother reading,
+ # so make it as educational and exemplary as possible!
+
+=head1 DESCRIPTION
+
+A full description of the module and its features.
+May include numerous subsections (i.e. =head2, =head3, etc).
+
+=head1 METHODS
+
+An object of this class represents...
+
+Below is a list of all public methods:
+
+error
+
+ Description:
+ Arguments:
+ Returns:
+ Example:
+ Exceptions:
+ Status: [Stable|Medium Risk|At Risk]
+
+
+
+=head1 BUGS AND LIMITATIONS
+
+A list of known problems with the module, together with some indication of
+whether they are likely to be fixed in an upcoming release.
+
+=head1 AUTHOR
+
+[name], Ensembl Web Team
+Support enquiries: helpdesk at ensembl.org
+
+=head1 COPYRIGHT
+
+See http://www.ensembl.org/info/about/code_licence.html
+
+
+__END__
+
+=head1 NAME
+
+SiteDefs
+
+=head1 SYNOPSIS
+
+ use <path>::SiteDefs;
+ # Brief but working code example(s) here showing the most common usage
+
+ # This section will be as far as many users bother reading,
+ # so make it as educational and exemplary as possible!
+
+=head1 DESCRIPTION
+
+A full description of the module and its features.
+May include numerous subsections (i.e. =head2, =head3, etc).
+
+=head1 METHODS
+
+An object of this class represents...
+
+Below is a list of all public methods:
+
+error
+
+ Description:
+ Arguments:
+ Returns:
+ Example:
+ Exceptions:
+ Status: [Stable|Medium Risk|At Risk]
+
+
+
+=head1 BUGS AND LIMITATIONS
+
+A list of known problems with the module, together with some indication of
+whether they are likely to be fixed in an upcoming release.
+
+=head1 AUTHOR
+
+[name], Ensembl Web Team
+Support enquiries: helpdesk at ensembl.org
+
+=head1 COPYRIGHT
+
+See http://www.ensembl.org/info/about/code_licence.html
+1;
Added: trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/pluginSiteDefs.pm
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/pluginSiteDefs.pm (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/pluginSiteDefs.pm 2010-08-26 22:00:33 UTC (rev 5188)
@@ -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;
Modified: trunk/packages/ensembl/ensembl/57/debian/init.d
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/init.d 2010-08-26 20:14:19 UTC (rev 5187)
+++ trunk/packages/ensembl/ensembl/57/debian/init.d 2010-08-26 22:00:33 UTC (rev 5188)
@@ -87,6 +87,12 @@
case $1 in
start)
+ for d in var/log/ensembl/logs /var/cache/ensembl/img-cache /var/tmp/ensembl/img-tmp /var/tmp/ensembl/tmp
+ do
+ if [ ! -d "$d" ]; then mkdir -p "$d"; fi
+ chown nobody.nogroup "$d"
+ chmod 755 "$d"
+ done
log_daemon_msg "Starting web server" "ensembl"
if $APACHE2CTL start; then
log_end_msg 0
Added: trunk/packages/ensembl/ensembl/57/debian/patches/MULTI.ini.notforrelease57.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/MULTI.ini.notforrelease57.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/MULTI.ini.notforrelease57.patch 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,13 @@
+Index: ensembl-57/conf/ini-files/MULTI.ini
+===================================================================
+--- ensembl-57.orig/conf/ini-files/MULTI.ini 2010-08-26 23:21:04.556642522 +0200
++++ ensembl-57/conf/ini-files/MULTI.ini 2010-08-26 23:21:41.700624359 +0200
+@@ -5,7 +5,7 @@
+ ENSEMBL_INSTITUTE_2 = <a href="http://www.ebi.ac.uk/" rel="external"><img src="/i/mid-ebi.gif" style="height:20px;width:65px" alt="EBI" title="European Bioinformatics Institute" /></a>
+
+ [databases]
+-DATABASE_WEBSITE = ensembl_website_%
++DATABASE_WEBSITE = ensembl_website_56
+ DATABASE_BLAST = ensembl_blast
+ DATABASE_COMPARA = ensembl_compara_%
+ # The following are extra configuration parameters for the databases
Added: trunk/packages/ensembl/ensembl/57/debian/patches/SiteDefs_ENSEMBL_BLOCK.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/SiteDefs_ENSEMBL_BLOCK.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/SiteDefs_ENSEMBL_BLOCK.patch 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,21 @@
+Index: ensembl-57/public-plugins/mirror/conf/SiteDefs.pm
+===================================================================
+--- ensembl-57.orig/public-plugins/mirror/conf/SiteDefs.pm 2010-08-26 23:30:46.445647758 +0200
++++ ensembl-57/public-plugins/mirror/conf/SiteDefs.pm 2010-08-26 23:31:28.364623343 +0200
+@@ -19,11 +19,11 @@
+ # $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_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
+ }
Added: trunk/packages/ensembl/ensembl/57/debian/patches/httpd.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/httpd.patch (rev 0)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/httpd.patch 2010-08-26 22:00:33 UTC (rev 5188)
@@ -0,0 +1,27 @@
+Index: ensembl-57/conf/httpd.conf
+===================================================================
+--- ensembl-57.orig/conf/httpd.conf 2010-08-26 23:27:49.484628908 +0200
++++ ensembl-57/conf/httpd.conf 2010-08-26 23:29:42.452635866 +0200
+@@ -14,20 +14,8 @@
+ ####
+ # 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 /usr/lib/apache2/modules/mod_perl.so
+-</IfModule>
+-<IfModule !deflate_module>
+-LoadModule deflate_module /usr/lib/apache2/modules/mod_deflate.so
+-</IfModule>
+-<IfModule !headers_module>
+-LoadModule headers_module /usr/lib/apache2/modules/mod_headers.so
+-</IfModule>
+-<IfModule !expires_module>
+-LoadModule expires_module /usr/lib/apache2/modules/mod_expires.so
+-</IfModule>
+-#
+-####
++
++Include /etc/apache2/mods-enabled/*.load
+
+ <Location / >
+ AddOutputFilterByType DEFLATE text/html text/plain text/xml text/javascript text/css application/x-javascript
Modified: trunk/packages/ensembl/ensembl/57/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-26 20:14:19 UTC (rev 5187)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-26 22:00:33 UTC (rev 5188)
@@ -6,3 +6,6 @@
mart_ini.patch
biodas_lite.patch
sessiondbconn.patch
+MULTI.ini.notforrelease57.patch
+httpd.patch
+SiteDefs_ENSEMBL_BLOCK.patch
Modified: trunk/packages/ensembl/ensembl/57/debian/postinst
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-26 20:14:19 UTC (rev 5187)
+++ trunk/packages/ensembl/ensembl/57/debian/postinst 2010-08-26 22:00:33 UTC (rev 5188)
@@ -31,6 +31,12 @@
grant all privileges on ensembl_web_user_db.* to ensembl at localhost identified by 'ensembl';
EOMYSQL
zcat /usr/share/doc/ensembl/ensembl_web_user_db.sql.gz | mysql -uensembl -pensembl ensembl_web_user_db
+ for d in var/log/ensembl/logs /var/cache/ensembl/img-cache /var/tmp/ensembl/img-tmp /var/tmp/ensembl/tmp
+ do
+ if [ ! -d "$d" ]; then mkdir -p "$d"; fi
+ chown nobody.nogroup "$d"
+ chmod 755 "$d"
+ done
;;
abort-upgrade|abort-remove|abort-deconfigure)
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-26 20:14:19 UTC (rev 5187)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-26 22:00:33 UTC (rev 5188)
@@ -9,6 +9,8 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+DESTDIR=$(CURDIR)/debian/ensembl
+
configure: configure-stamp
configure-stamp:
# nothing to be configured
@@ -20,12 +22,17 @@
touch build-stamp
install: install-copying install-paths
+ # copying files that are considered too different from the original
+ # and/or the original too variable across releases to be patched
+ cp ensembl.overwrites/Plugins.pm-dist $(DESTDIR)/usr/share/ensembl/conf/
+ cp ensembl.overwrites/confSiteDefs.pm $(DESTDIR)/usr/share/ensembl/conf/SiteDefs.pm
+ cp ensembl.overwrites/pluginSiteDefs.pm $(DESTDIR)/usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
install-copying:
dh_testdir
dh_testroot
dh_prep
- d=$(CURDIR)/debian/ensembl/usr/share/ensembl ; \
+ d=$(DESTDIR)/usr/share/ensembl ; \
if [ ! -d "$$d" ]; then \
echo "Creating directory '$$d'." ; \
mkdir -p "$$d" ; \
@@ -35,7 +42,7 @@
ensembl-functgenomics ensembl-variation \
htdocs modules perl public-plugins utils \
$$d
- d=$(CURDIR)/debian/ensembl/usr/bin ; \
+ d=$(DESTDIR)/usr/bin ; \
if [ ! -d "$$d" ]; then \
echo "Creating directory '$$d'." ; \
mkdir -p "$$d" ; \
@@ -44,7 +51,7 @@
touch $@
install-paths: install-copying
- d=$(CURDIR)/debian/ensembl/usr/share/ensembl ; \
+ d=$(DESTDIR)/usr/share/ensembl ; \
if [ ! -d "$$d" ]; then \
echo "Directory '$$d' not existing. Quitting." ; \
exit 1; \
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