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 <[email protected]> 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@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@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: [email protected]\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@ADDRESS>\n" "Language-Team: LANGUAGE <[email protected]>\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.$$ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
