[med-svn] r6780 - in trunk/packages/ensembl/ensembl: . 62/debian 62/debian/ensembl.overwrites 62/debian/patches 62/debian/po
Madhu Donepudi
mdonepudi-guest at alioth.debian.org
Thu May 5 10:50:37 UTC 2011
Author: mdonepudi-guest
Date: 2011-05-05 10:50:35 +0000 (Thu, 05 May 2011)
New Revision: 6780
Added:
trunk/packages/ensembl/ensembl/62/
Modified:
trunk/packages/ensembl/ensembl/62/debian/changelog
trunk/packages/ensembl/ensembl/62/debian/control
trunk/packages/ensembl/ensembl/62/debian/copyright
trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/confSiteDefs.pm
trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/pluginSiteDefs.pm
trunk/packages/ensembl/ensembl/62/debian/patches/httpd.patch
trunk/packages/ensembl/ensembl/62/debian/patches/sessiondbconn.patch
trunk/packages/ensembl/ensembl/62/debian/po/templates.pot
trunk/packages/ensembl/ensembl/62/debian/prepare_ensembl_source_packages.sh
Log:
Updated to Ensembl version62
Modified: trunk/packages/ensembl/ensembl/62/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/changelog 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/changelog 2011-05-05 10:50:35 UTC (rev 6780)
@@ -1,3 +1,9 @@
+ensembl (62-1) experimental; urgency=low
+
+ * Updated to Ensembl version 62
+
+ -- Madhu Donepudi <madhu at eaglegenomics.com> Tue, 19 Apr 2011 06:32:48 -0400
+
ensembl (57-7) experimental; urgency=low
* Adding sources of version 2.6.1 for Jalview
Modified: trunk/packages/ensembl/ensembl/62/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/control 2011-05-05 10:50:35 UTC (rev 6780)
@@ -7,8 +7,8 @@
Build-Depends: debhelper (>= 7.0.50~), po-debconf
Standards-Version: 3.9.1.0
Homepage: http://www.ensembl.org
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ensembl/ensembl/57/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ensembl/ensembl/57/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ensembl/ensembl/62/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ensembl/ensembl/62/
Package: ensembl
Architecture: all
@@ -17,7 +17,7 @@
Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl, libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl, libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl, libdata-uuid-libuuid-perl, libgd-text-perl, libhash-merge-perl, libhtml-parser-perl, liblist-moreutils-perl, liblog-log4perl-perl, libmailtools-perl, libwww-curl-perl, libapache2-mod-perl2, libnumber-format-perl, libgd-gd2-noxpm-perl, libpdf-api2-perl, libsys-hostname-long-perl, libtemplate-plugin-number-format-perl, libxml-dom-perl, libxml-rss-perl, libxml-simple-perl, libbsd-resource-perl, libxml-xpath-perl, libxml-atom-perl, libjson-perl, libclass-data-inheritable-perl, libconfig-inifiles-perl, libdevel-stacktrace-perl, libexception-class-perl, libhtml-template-perl, libimage-size-perl, libio-string-perl, libipc-run-perl, libxml-libxml-perl, libole-storage-lite-perl, libparse-recdescent-perl, libspreadsheet-writeexcel-perl, libmime-types-perl, libmath-bezier-perl, librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3|bioperl
Suggests: ksh | mksh | pdksh | zsh
Section: non-free/science
-Description: Installs a basic Ensembl 57 genome browser.
+Description: Installs a basic Ensembl 62 genome browser.
Ensembl is a joint project of the Sanger Center and the European
Bioinformatics Institute, an outstation of the European Molecular
Biology Laboratory, (EMBL-EBI) that are sharing a campus in Hinxton
Modified: trunk/packages/ensembl/ensembl/62/debian/copyright
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/copyright 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/copyright 2011-05-05 10:50:35 UTC (rev 6780)
@@ -8,7 +8,7 @@
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
+ ftp://ftp.ensembl.org/pub/release-62/mysql/ensembl_web_user_db/ensembl_web_user_db.sql.gz
Files: ensembl-compara/modules/Algorithm/Diff.pm
Modified: trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/confSiteDefs.pm
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/confSiteDefs.pm 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/confSiteDefs.pm 2011-05-05 10:50:35 UTC (rev 6780)
@@ -1,4 +1,3 @@
-#!/usr/bin/perl -w
###############################################################################
#
# Name: SiteDefs.pm
@@ -16,11 +15,12 @@
use vars qw ( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION
$APACHE_DIR
$APACHE_BIN
- $BIOPERL_DIR
+ $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
+ $OBJECT_TO_SCRIPT
$ENSEMBL_VERSION
$ENSEMBL_PLUGINS $ENSEMBL_PLUGIN_ROOTS
$ENSEMBL_TMPL_CSS
@@ -64,7 +64,7 @@
$ENSEMBL_SPECIES
$ENSEMBL_PRIMARY_SPECIES
$ENSEMBL_SECONDARY_SPECIES
- $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL $ENSEMBL_STATIC_SERVER $ENSEMBL_STATIC_SERVERNAME $ENSEMBL_STATIC_BASE_URL
$ENSEMBL_SPECIES_ALIASES
$ENSEMBL_ENCRYPT_0
$ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
@@ -94,7 +94,7 @@
$ARCHIVE_VERSION
$BIOMART_URL
$MART_HELP_DESK
- %OBJECT_TO_SCRIPT
+ $OBJECT_TO_SCRIPT
%ENSEMBL_SETENV
@ENSEMBL_CONF_DIRS
@ENSEMBL_PERL_DIRS
@@ -105,15 +105,19 @@
$ENSEMBL_MART_ENABLED
$ENSEMBL_BLAST_ENABLED
$ENSEMBL_FLAG_NAMES
+ $SAMTOOLS_DIR
+ $SAMTOOLS_HTTP_PROXY
+ $MINI_BIOPERL_161_DIR
+ $UDC_CACHEDIR
);
use Sys::Hostname::Long;
use Exporter();
@ISA=qw(Exporter);
-$VERSION = 57;
-$ARCHIVE_VERSION = "Mar2010"; # Change this to the archive site for this version
-$ENSEMBL_RELEASE_DATE = 'Mar 2010';
+$VERSION = 62;
+$ARCHIVE_VERSION = "Apr2011"; # Change this to the archive site for this version
+$ENSEMBL_RELEASE_DATE = 'April 2011';
$ENSEMBL_MIN_SPARE_SERVERS = 5;
$ENSEMBL_MAX_SPARE_SERVERS = 20;
@@ -154,7 +158,13 @@
$ENSEMBL_SERVERROOT = '.' unless $ENSEMBL_SERVERROOT;
$APACHE_DIR = "$ENSEMBL_SERVERROOT/apache2";
-$BIOPERL_DIR = "$ENSEMBL_SERVERROOT/bioperl-live";
+$SAMTOOLS_DIR = "$ENSEMBL_SERVERROOT/samtools";
+$SAMTOOLS_HTTP_PROXY = '';
+
+$UDC_CACHEDIR = '';
+
+$BIOPERL_DIR ||= "$ENSEMBL_SERVERROOT/bioperl-live";
+$MINI_BIOPERL_161_DIR ||= "$ENSEMBL_SERVERROOT/mini-bioperl-161";
#warn "$ENSEMBL_SERVERROOT";
## Define Plugin directories....
eval qq(require '$ENSEMBL_SERVERROOT/$CONF_DIR/Plugins.pm');
@@ -172,8 +182,10 @@
# 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_USER = getpwuid($>); # Auto-set web serveruser
+#$ENSEMBL_GROUP = getgrgid($)); # Auto-set web server group
+$ENSEMBL_USER = "nobody";
+$ENSEMBL_GROUP = "nogroup";
$ENSEMBL_SERVERADMIN = 'webmaster@mydomain.org';
$ENSEMBL_HELPDESK_EMAIL = $ENSEMBL_SERVERADMIN;
@@ -255,6 +267,7 @@
$ENSEMBL_BLASTSCRIPT = undef;
$ENSEMBL_REGISTRY = undef;
$ENSEMBL_PRIVATE_AUTH = undef;
+
####################
# Environment variables to set using the SetEnv directive
%ENSEMBL_SETENV =
@@ -346,41 +359,39 @@
$ENSEMBL_LONGPROCESS_MINTIME = 10;
## ALLOWABLE DATA OBJECTS
-%OBJECT_TO_SCRIPT = (
- Config => 'config',
- Component => 'component',
- Zmenu => 'zmenu',
- Blast => 'blast',
+$OBJECT_TO_SCRIPT = {
+ Config => 'Config',
+ Component => 'Component',
+ ZMenu => 'ZMenu',
+ psychic => 'Psychic',
+ autocomplete => 'AutoComplete',
+
+ Export => 'Export',
- Gene => 'action',
- Transcript => 'action',
- Location => 'action',
- Variation => 'action',
- Regulation => 'action',
- Server => 'action',
- Info => 'action',
- Search => 'action',
- UniSearch => 'action',
- News => 'action',
+ Gene => 'Page',
+ Transcript => 'Page',
+ Location => 'Page',
+ Variation => 'Page',
+ StructuralVariation => 'Page',
+ Regulation => 'Page',
+ Marker => 'Page',
+ GeneTree => 'Page',
+ LRG => 'Page',
+ Blast => 'Page',
+ Tools => 'Page',
+ Info => 'Page',
+ Search => 'Page',
+ UniSearch => 'Page',
+ News => 'Page',
- Account => 'modal',
- UserData => 'modal',
- Help => 'modal',
- Export => 'modal',
-);
+ Account => 'Modal',
+ UserData => 'Modal',
+ Help => '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";
@@ -502,6 +513,7 @@
$ENSEMBL_SERVERROOT.'/ensembl-external/modules',
$ENSEMBL_SERVERROOT.'/biomart-perl/lib',
$BIOPERL_DIR,
+ $MINI_BIOPERL_161_DIR,
$ENSEMBL_SERVERROOT.'/modules',
);
@@ -512,7 +524,6 @@
unshift @ENSEMBL_HTDOCS_DIRS, $dir.'/htdocs';
unshift @$ENSEMBL_PLUGIN_ROOTS, $name;
push @ENSEMBL_CONF_DIRS, $dir.'/conf';
- unshift @ENSEMBL_LIB_DIRS, $dir.'/modules';
}
@T = @{$ENSEMBL_PLUGINS||[]}; ## But these have to go on in normal order...
@@ -530,7 +541,7 @@
## And one without the _ in...
$ENSEMBL_SPECIES_ALIASES = {};
-$ENSEMBL_DATASETS = [ sort keys %__species_aliases ];
+$ENSEMBL_DATASETS ||= [ sort keys %__species_aliases ];
foreach my $name ( @$ENSEMBL_DATASETS ) {
foreach my $alias ( @{$__species_aliases{$name}} ) {
@@ -567,24 +578,31 @@
$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 $ENSEMBL_SITE_DIR;
+$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 $ENSEMBL_SITE_DIR;
+
+$ENSEMBL_STATIC_SERVERNAME = $ENSEMBL_STATIC_SERVER || $ENSEMBL_SERVERNAME;
+$ENSEMBL_STATIC_SERVER = "$ENSEMBL_PROTOCOL://$ENSEMBL_STATIC_SERVER" if $ENSEMBL_STATIC_SERVER;
+$ENSEMBL_STATIC_BASE_URL = $ENSEMBL_STATIC_SERVER || $ENSEMBL_BASE_URL;
+
$MART_ENSEMBL_LINKS = $ENSEMBL_BASE_URL;
-$MART_HELP_DESK = $ENSEMBL_SITE_URL.'default/helpview';
-$ENSEMBL_TEMPLATE_ROOT = $ENSEMBL_SERVERROOT.'/biomart-perl/conf';
+$MART_HELP_DESK = $ENSEMBL_SITE_URL . 'default/helpview';
+$ENSEMBL_TEMPLATE_ROOT = $ENSEMBL_SERVERROOT . '/biomart-perl/conf';
####################
# Export by default
####################
@EXPORT = qw(
$ENSEMBL_FLAG_NAMES
+ $APACHE_BIN
$APACHE_DIR
$BIOPERL_DIR
$CGI_POST_MAX
@@ -625,12 +643,15 @@
$ENSEMBL_CONFIG_FILENAME
$ENSEMBL_CONFIG_BUILD
$ENSEMBL_HAS_C_EXTENSIONS
+ $OBJECT_TO_SCRIPT
$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
+ $SAMTOOLS_HTTP_PROXY
+ $UDC_CACHEDIR
);
############################
@@ -638,11 +659,13 @@
############################
@EXPORT_OK = qw(
$ENSEMBL_FLAG_NAMES
+ $APACHE_BIN
$APACHE_DIR
$CGI_POST_MAX
- $BIOPERL_DIR
+ $BIOPERL_DIR
$ENSEMBL_HELPDESK_EMAIL
$ENSEMBL_MAIL_SERVER
+ $OBJECT_TO_SCRIPT
$ENSEMBL_VERSION
$ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
$ENSEMBL_PLUGIN_ROOTS
@@ -652,7 +675,6 @@
@ENSEMBL_HTDOCS_DIRS
@ENSEMBL_LIB_DIRS
$ENSEMBL_SHORTEST_ALIAS
-
$ENSEMBL_TMPL_CSS
$ENSEMBL_PAGE_CSS
$ENSEMBL_IMAGE_WIDTH
@@ -695,7 +717,7 @@
$ENSEMBL_SPECIES
$ENSEMBL_PRIMARY_SPECIES
$ENSEMBL_SECONDARY_SPECIES
- $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL $ENSEMBL_STATIC_SERVER $ENSEMBL_STATIC_SERVERNAME $ENSEMBL_STATIC_BASE_URL
$ENSEMBL_SPECIES_ALIASES
$ENSEMBL_ENCRYPT_0
$ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
@@ -734,6 +756,7 @@
%EXPORT_TAGS = (
ALL => [qw(
$ENSEMBL_FLAG_NAMES
+ $APACHE_BIN
$APACHE_DIR
$CGI_POST_MAX
$BIOPERL_DIR
@@ -778,7 +801,7 @@
$ENSEMBL_SPECIES
$ENSEMBL_PRIMARY_SPECIES
$ENSEMBL_SECONDARY_SPECIES
- $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL
+ $ENSEMBL_BASE_URL $ENSEMBL_SITE_DIR $ENSEMBL_SITE_URL $ENSEMBL_STATIC_SERVER $ENSEMBL_STATIC_SERVERNAME $ENSEMBL_STATIC_BASE_URL
$ENSEMBL_SPECIES_ALIASES
$ENSEMBL_ENCRYPT_0
$ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
@@ -806,6 +829,7 @@
$ENSEMBL_APACHE_RELOAD
$ENSEMBL_SITETYPE
$ARCHIVE_VERSION
+ $OBJECT_TO_SCRIPT
$ENSEMBL_PRIVATE_AUTH $ENSEMBL_REGISTRY
$ENSEMBL_VERSION
$ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
@@ -829,6 +853,7 @@
$ENSEMBL_PLUGIN_ROOTS
$ENSEMBL_HELPDESK_EMAIL
$ENSEMBL_MAIL_SERVER
+ $OBJECT_TO_SCRIPT
$ENSEMBL_VERSION
$ENSEMBL_RELEASE_DATE $ENSEMBL_MIN_SPARE_SERVERS $ENSEMBL_MAX_SPARE_SERVERS $ENSEMBL_START_SERVERS
$ENSEMBL_TMPL_CSS
@@ -879,71 +904,60 @@
$ENSEMBL_MART_ENABLED
$ENSEMBL_BLAST_ENABLED
)],
-
+
APACHE => [qw(
- $ENSEMBL_FLAG_NAMES
+ $APACHE_BIN
$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_COOKIEHOST
+ $ENSEMBL_CUSTOMLOG
+ $ENSEMBL_DEBUG_FLAGS
$ENSEMBL_ENCRYPT_0
- $ENSEMBL_ENCRYPT_1 $ENSEMBL_ENCRYPT_EXPIRY $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ENCRYPT_1
$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_ENCRYPT_EXPIRY
+ $ENSEMBL_ENCRYPT_REFRESH
+ $ENSEMBL_ERRORLOG
+ $ENSEMBL_GROUP
+ @ENSEMBL_HTDOCS_DIRS
+ $ENSEMBL_IMAGE_WIDTH
+ @ENSEMBL_LIB_DIRS
$ENSEMBL_LONGPROCESS_MINTIME
- $ENSEMBL_SITETYPE
- $ENSEMBL_SHORTEST_ALIAS
- $ARCHIVE_VERSION
- $MART_ENSEMBL_LINKS
+ $ENSEMBL_MAX_SPARE_SERVERS
$ENSEMBL_MART_ENABLED
- $ENSEMBL_BLAST_ENABLED
+ $ENSEMBL_MIN_SPARE_SERVERS
+ @ENSEMBL_PERL_DIRS
+ $ENSEMBL_PIDFILE
+ $ENSEMBL_PLUGINS
+ $ENSEMBL_PORT
+ $ENSEMBL_PRIMARY_SPECIES
+ $ENSEMBL_PRIVATE_AUTH
+ $ENSEMBL_SERVER
+ $ENSEMBL_SERVERADMIN
+ $ENSEMBL_SERVERNAME
+ $ENSEMBL_SERVERROOT
+ $ENSEMBL_SESSION_COOKIE
+ %ENSEMBL_SETENV
+ $ENSEMBL_SPECIES_ALIASES
+ $ENSEMBL_START_SERVERS
+ $ENSEMBL_TMP_CREATE
+ $ENSEMBL_TMP_DELETE
+ $ENSEMBL_TMP_DIR_BLAST
+ $ENSEMBL_TMP_DIR_IMG
+ $ENSEMBL_TMP_URL_IMG
+ $ENSEMBL_USER
+ $ENSEMBL_USER_COOKIE
+ $OBJECT_TO_SCRIPT
+ $SAMTOOLS_HTTP_PROXY
+ $UDC_CACHEDIR
)],
);
+__END__
+=head1 NAME
-__END__
-
-=head1 NAME
-
SiteDefs
=head1 SYNOPSIS
Modified: trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/pluginSiteDefs.pm
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.overwrites/pluginSiteDefs.pm 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/ensembl.overwrites/pluginSiteDefs.pm 2011-05-05 10:50:35 UTC (rev 6780)
@@ -1,31 +1,82 @@
-package EnsEMBL::Mirror::SiteDefs;
+package EnsEMBL::Ensembl::SiteDefs;
use strict;
sub update_conf {
-$SiteDefs::ENSEMBL_PORT = __USER_ENSEMBL_PORT__;
-$SiteDefs::ENSEMBL_USER = 'nobody';
-$SiteDefs::ENSEMBL_GROUP = 'nogroup';
+ $SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'Homo_sapiens'; # Default species
+ $SiteDefs::ENSEMBL_SECONDARY_SPECIES = 'Mus_musculus'; # Secondary species
-# $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';
+## 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
-# $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 = '__USER_ENS_DB_NAME__';
- $SiteDefs::ENSEMBL_USERDB_USER = '__USER_ENS_DB_USER__';
- $SiteDefs::ENSEMBL_USERDB_HOST = '__USER_ENS_DB_HOST__';
- $SiteDefs::ENSEMBL_USERDB_PORT = __USER_ENS_DB_PORT__;
- $SiteDefs::ENSEMBL_USERDB_PASS = '__USER_ENS_DB_PWD__';
-
-$SiteDefs::ENSEMBL_LOGINS = 0; ## Change to 1 to turn user logins on
+#-------------------- mammals
+ $SiteDefs::__species_aliases{ 'Ailuropoda_melanoleuca' } = [qw(am amel panda)];
+ $SiteDefs::__species_aliases{ 'Bos_taurus' } = [qw(bt btau cow moo)];
+ $SiteDefs::__species_aliases{ 'Callithrix_jacchus' } = [qw(cj cjac marmoset)];
+ $SiteDefs::__species_aliases{ 'Canis_familiaris' } = [qw(cf cfam dog)];
+ $SiteDefs::__species_aliases{ 'Cavia_porcellus' } = [qw(cp cpor guineapig)];
+ $SiteDefs::__species_aliases{ 'Choloepus_hoffmanni' } = [qw(ch chof sloth)];
+ $SiteDefs::__species_aliases{ 'Dasypus_novemcinctus' } = [qw(dn dnov dasypus armadillo)];
+ $SiteDefs::__species_aliases{ 'Dipodomys_ordii' } = [qw(do kangaroorat)];
+ $SiteDefs::__species_aliases{ 'Echinops_telfairi' } = [qw(et etel echinops tenrec)];
+ $SiteDefs::__species_aliases{ 'Equus_caballus' } = [qw(ec horse)];
+ $SiteDefs::__species_aliases{ 'Erinaceus_europaeus' } = [qw(ee eeur hedgehog)];
+ $SiteDefs::__species_aliases{ 'Gorilla_gorilla' } = [qw(ggo kong gorilla)];
+ $SiteDefs::__species_aliases{ 'Felis_catus' } = [qw(fc fcat cat)];
+ $SiteDefs::__species_aliases{ 'Gorilla_gorilla' } = [qw(gg ggor gorilla kong)];
+ $SiteDefs::__species_aliases{ 'Homo_sapiens' } = [qw(hs hsap human man default)];
+ $SiteDefs::__species_aliases{ 'Loxodonta_africana' } = [qw(la lafr elephant africana loxodontai hathi nellie dumbo)];
+ $SiteDefs::__species_aliases{ 'Oryctolagus_cuniculus' } = [qw(oc ocun rabbit bugs bunny hutch harvey)];
+ $SiteDefs::__species_aliases{ 'Macaca_mulatta' } = [qw(mmu mmul rhesus macaque macaca)];
+ $SiteDefs::__species_aliases{ 'Macropus_eugenii' } = [qw(me meug wallaby)];
+ $SiteDefs::__species_aliases{ 'Microcebus_murinus' } = [qw(mmur lemur)];
+ $SiteDefs::__species_aliases{ 'Monodelphis_domestica' } = [qw(md mdom monodelphis opossum)];
+ $SiteDefs::__species_aliases{ 'Mus_musculus' } = [qw(mm mmus mouse mus)];
+ $SiteDefs::__species_aliases{ 'Myotis_lucifugus' } = [qw(ml mluc microbat myotis)];
+ $SiteDefs::__species_aliases{ 'Nomascus_leucogenys' } = [qw(nl nleu gibbon nomascus)];
+ $SiteDefs::__species_aliases{ 'Ochotona_princeps' } = [qw(op pika pikachu)];
+ $SiteDefs::__species_aliases{ 'Ornithorhynchus_anatinus' } = [qw(oa oana platypus)];
+ $SiteDefs::__species_aliases{ 'Otolemur_garnettii' } = [qw(og ogar bushbaby otolemur)];
+ $SiteDefs::__species_aliases{ 'Pan_troglodytes' } = [qw(pt ptro chimp)];
+ $SiteDefs::__species_aliases{ 'Pongo_abelii' } = [qw(pp Pongo_pygmaeus orang orangutan librarian ook)];
+ $SiteDefs::__species_aliases{ 'Procavia_capensis' } = [qw(pc hyrax dassy dassie pimbi)];
+ $SiteDefs::__species_aliases{ 'Pteropus_vampyrus' } = [qw(pv megabat flyingfox)];
+ $SiteDefs::__species_aliases{ 'Rattus_norvegicus' } = [qw(rn rnor rat)];
+ $SiteDefs::__species_aliases{ 'Sorex_araneus' } = [qw(sa shrew)];
+ $SiteDefs::__species_aliases{ 'Spermophilus_tridecemlineatus' } = [qw(st stri squirrel spermophilus)];
+ $SiteDefs::__species_aliases{ 'Sus_scrofa' } = [qw(ss sscr pig sus oink porky)];
+ $SiteDefs::__species_aliases{ 'Tarsius_syrichta' } = [qw(ts tarsier gremlin)];
+ $SiteDefs::__species_aliases{ 'Tupaia_belangeri' } = [qw(tb tbel treeshrew shrew)];
+ $SiteDefs::__species_aliases{ 'Tursiops_truncatus' } = [qw(tt dolphin flipper)];
+ $SiteDefs::__species_aliases{ 'Vicugna_pacos' } = [qw(lp alpaca)];
+#-------------------- birds
+ $SiteDefs::__species_aliases{ 'Gallus_gallus' } = [qw(gg ggal chicken)];
+ $SiteDefs::__species_aliases{ 'Meleagris_gallopavo' } = [qw(mg mgal turkey meleagris)];
+ $SiteDefs::__species_aliases{ 'Taeniopygia_guttata' } = [qw(tg taegut taeniopygia zebrafinch)];
+#-------------------- fish
+ $SiteDefs::__species_aliases{ 'Danio_rerio' } = [qw(dr drer zfish zebrafish)];
+ $SiteDefs::__species_aliases{ 'Gasterosteus_aculeatus' } = [qw(ga gacu stickleback gasterosteus)];
+ $SiteDefs::__species_aliases{ 'Oryzias_latipes' } = [qw(ol olat medaka)];
+ $SiteDefs::__species_aliases{ 'Takifugu_rubripes' } = [qw(fr trub ffish fugu takifugu f_rubripes fugu_rubripes)];
+ $SiteDefs::__species_aliases{ 'Tetraodon_nigroviridis' } = [qw(tn tnig tetraodon)];
+#-------------------- amphibians
+ $SiteDefs::__species_aliases{ 'Xenopus_tropicalis' } = [qw(xt xtro xenopus frog)];
+#-------------------- reptiles
+ $SiteDefs::__species_aliases{ 'Anolis_carolinensis' } = [qw(ac anolis anole lizard)];
+#-------------------- flies
+# $SiteDefs::__species_aliases{ 'Aedes_aegypti' } = [qw(aa aaeg aedes )];
+# $SiteDefs::__species_aliases{ 'Anopheles_gambiae' } = [qw(ag agam mosquito mos anopheles)];
+# $SiteDefs::__species_aliases{ 'Apis_mellifera' } = [qw(am amel honeybee bee)];
+ $SiteDefs::__species_aliases{ 'Drosophila_melanogaster' } = [qw(dm dmel fly)];
+#-------------------- worms
+# $SiteDefs::__species_aliases{ 'Caenorhabditis_briggsae' } = [qw(cb cbri briggsae)];
+ $SiteDefs::__species_aliases{ 'Caenorhabditis_elegans' } = [qw(ce cele worm elegans)];
+ $SiteDefs::__species_aliases{ 'Ciona_intestinalis' } = [qw(ci cint seasquirti cionai)];
+ $SiteDefs::__species_aliases{ 'Ciona_savignyi' } = [qw(cs csav seasquirts cionas)];
+#-------------------- yeast
+ $SiteDefs::__species_aliases{ 'Saccharomyces_cerevisiae' } = [qw(sc scer yeast saccharomyces )];
+ $SiteDefs::__species_aliases{ 'Ailuropoda_melanoleuca' } = [qw(panda giant_panda)];
}
1;
Modified: trunk/packages/ensembl/ensembl/62/debian/patches/httpd.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/httpd.patch 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/patches/httpd.patch 2011-05-05 10:50:35 UTC (rev 6780)
@@ -1,8 +1,8 @@
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 @@
+--- 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
+@@ -14,18 +14,8 @@
####
# Load the required apache modules (unless built-into httpd)
# The .so files can be built with apxs if missing
@@ -18,10 +18,8 @@
-<IfModule !expires_module>
-LoadModule expires_module 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/62/debian/patches/sessiondbconn.patch
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/sessiondbconn.patch 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/patches/sessiondbconn.patch 2011-05-05 10:50:35 UTC (rev 6780)
@@ -1,15 +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
+--- 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,
+- $species_defs->multidb->{'DATABASE_SESSION'}{'USER'} || $species_defs->DATABASE_WRITE_USER,
+- $species_defs->multidb->{'DATABASE_SESSION'}{'PASS'} || $species_defs->DATABASE_WRITE_PASS,
++ $species_defs->multidb->{'DATABASE_SESSION'}{'USER'} || $species_defs->ENSEMBL_USERDB_USER,
++ $species_defs->multidb->{'DATABASE_SESSION'}{'PASS'} || $species_defs->ENSEMBL_USERDB_PASS,
{
RaiseError => 1,
PrintError => 1,
Modified: trunk/packages/ensembl/ensembl/62/debian/po/templates.pot
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/po/templates.pot 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/po/templates.pot 2011-05-05 10:50:35 UTC (rev 6780)
@@ -8,11 +8,10 @@
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: ensembl at packages.debian.org\n"
-"POT-Creation-Date: 2011-02-02 00:07+0100\n"
+"POT-Creation-Date: 2011-04-20 12:52-0400\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
"Language-Team: LANGUAGE <LL at li.org>\n"
-"Language: \n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=CHARSET\n"
"Content-Transfer-Encoding: 8bit\n"
@@ -27,9 +26,10 @@
#. Description
#: ../ensembl.templates:1001
msgid ""
-"Ensembl presents itself to the user via a web server. When there are "
-"multiple web pages on the same server, it is not unlikely that Ensembl "
-"should have a different than the default port 80."
+"The Ensembl web interface runs apache underneath. If no other service is "
+"running on the same machine, the port should most likely be 80, just as with "
+"regular web services. We presume another web server and/or tomcat (8080) to "
+"be already running and have chosen port 8000 as a default."
msgstr ""
#. Type: string
@@ -40,13 +40,40 @@
#. Type: string
#. Description
+#. Type: string
+#. Description
+#. Type: string
+#. Description
+#. Type: string
+#. Description
+#. Type: string
+#. Description
+#. Type: boolean
+#. Description
+#. Type: boolean
+#. Description
+#. Type: string
+#. Description
+#. Type: password
+#. Description
+#: ../ensembl.templates:2001 ../ensembl.templates:3001
+#: ../ensembl.templates:4001 ../ensembl.templates:5001
+#: ../ensembl.templates:6001 ../ensembl.templates:7001
+#: ../ensembl.templates:8001 ../ensembl.templates:9001
+#: ../ensembl.templates:10001
+msgid ""
+"The Ensembl web interface has the option to store temporary data locally, so "
+"it does not need to transfer all information all the time from one web page "
+"to another but has those readily available in a database."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:2001
msgid ""
-"The local installation of Ensembl needs a MySQL Database server to store "
-"user-associated data. Please specify the hostname of the server here. Enter "
-"it in the same way that you would use to log into that machine when using it "
-"manually from the server and test that you have all the right access "
-"permissions."
+"Please specify the IP number or hostname of the server here. Enter it in the "
+"same way that you would use to log into that machine when using it manually "
+"from the server and test that you have all the right access permissions."
msgstr ""
#. Type: string
@@ -58,7 +85,10 @@
#. Type: string
#. Description
#: ../ensembl.templates:3001
-msgid "The port of the local MySQL database."
+msgid ""
+"For most installations, this database will be MySQL, which by default "
+"listens to port 3306. This may be different if that machine has another "
+"instance of MySQL already."
msgstr ""
#. Type: string
@@ -71,8 +101,9 @@
#. Description
#: ../ensembl.templates:4001
msgid ""
-"The local database to store user associated data for Ensembl shall have a "
-"name."
+"If you change this name to something else than the default, then you must be "
+"a real advanced user and do not need any further description ob what this "
+"thing is doing."
msgstr ""
#. Type: string
@@ -84,11 +115,26 @@
#. Type: string
#. Description
#: ../ensembl.templates:5001
-msgid "The username under which the database can be accessed."
+msgid ""
+"This parameter sets the username under which the database can be accessed. "
+"Security sensitive admins may decide to specify a database user for the "
+"local database that differs from the default. But the Ensembl installation "
+"is complex, i.e. you may into unexpected issues when diverging from the "
+"default."
msgstr ""
#. Type: string
#. Description
+#. Type: string
+#. Description
+#: ../ensembl.templates:5001 ../ensembl.templates:6001
+msgid ""
+"Please start with the default as a start. To increase security, allow access "
+"only from the machine that runs the web server."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../ensembl.templates:6001
msgid "MySQL password for web user db:"
msgstr ""
@@ -96,7 +142,11 @@
#. Type: string
#. Description
#: ../ensembl.templates:6001
-msgid "The password with which to access the local Ensembl database."
+msgid ""
+"Security sensitive admins may decide to specify a password for that "
+"database' user that differs from the default. But the Ensembl installation "
+"is complex, i.e. you may into unexpected issues when diverging from the "
+"default."
msgstr ""
#. Type: boolean
@@ -109,18 +159,13 @@
#. Description
#: ../ensembl.templates:7001
msgid ""
-"When installing Ensembl, the local database may already exist, e.g. from a "
-"previous installation."
+"Please specify with 'Y' if the database does already exist. If you answer "
+"with 'N', it will be created for you. If 'Y', you will be asked if the "
+"existing data should be overwritten."
msgstr ""
#. Type: boolean
#. Description
-#: ../ensembl.templates:7001
-msgid "True if the web user db already exists."
-msgstr ""
-
-#. Type: boolean
-#. Description
#: ../ensembl.templates:8001
msgid "If existing, should the web user db be kept?"
msgstr ""
@@ -136,7 +181,9 @@
#. Type: boolean
#. Description
#: ../ensembl.templates:8001
-msgid "True if the web user db already exists and should be kept:"
+msgid ""
+"Anser with 'Y' if the previous data should be kept. This only works when "
+"there are no changes done to the database schema. If not sure, answer 'N'."
msgstr ""
#. Type: string
@@ -149,12 +196,22 @@
#. Description
#: ../ensembl.templates:9001
msgid ""
-"When a new database shall be created, one needs a user with the permissions "
-"to perform so."
+"To create the database you need special permissions that this admin user "
+"shall have."
msgstr ""
+#. Type: string
+#. Description
#. Type: password
#. Description
+#: ../ensembl.templates:9001 ../ensembl.templates:10001
+msgid ""
+"This parameter is only required if the user database does not yet exist or "
+"it was previously opted that this shall be created again."
+msgstr ""
+
+#. Type: password
+#. Description
#: ../ensembl.templates:10001
msgid "MySQL admin password for creating the web user db if it doesn't exist:"
msgstr ""
@@ -163,7 +220,8 @@
#. Description
#: ../ensembl.templates:10001
msgid ""
-"The user with the right to create a new database most likely has a password."
+"This specifies the password with which the admin user can access the "
+"database."
msgstr ""
#. Type: boolean
@@ -176,13 +234,14 @@
#. Description
#: ../ensembl.templates:11001
msgid ""
-"When the database is available, the remaining question is how to perform "
-"with already existing tables."
+"Keeping the web user database means you don't have to recreate it, but you "
+"might want to drop and recreate the tables within it."
msgstr ""
#. Type: boolean
#. Description
#: ../ensembl.templates:11001
msgid ""
-"True if the web user db already exists and the data in it should be kept:"
+"If you didn't keep the database, you don't need to answer this. If the "
+"database didn't already exist, you don't need to answer."
msgstr ""
Modified: trunk/packages/ensembl/ensembl/62/debian/prepare_ensembl_source_packages.sh
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/prepare_ensembl_source_packages.sh 2011-05-05 10:09:31 UTC (rev 6779)
+++ trunk/packages/ensembl/ensembl/62/debian/prepare_ensembl_source_packages.sh 2011-05-05 10:50:35 UTC (rev 6780)
@@ -17,7 +17,7 @@
# All libraries must be of the same version - update them all or none
if [ -z "$ensemblversion" ]; then
- ensemblversion=57
+ ensemblversion=62
fi
downloaddir=$destdir/$ensemblversion.$$
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