hello Syed, I just installed biomart 0.6 standalone and it is working. But unfortunately I still get "ERROR: requested template missing" when running biomart in ensembl.
here is the output of configure.pl: [EMAIL PROTECTED]:/u1/ET/ensembl/ensembl/biomart-perl> perl bin/configure.pl -r conf/registryURLPointer.xml --clean Do you want to install in API only mode [y/n] [n]: Checking prerequisites ...[Looks good] APACHE: /u1/ET/ensembl/ensembl/apache2/bin/httpd HOST: localhost PORT: 9002 Use of uninitialized value in print at /u1/ET/ensembl/branch-ensembl-45/biomart-perl/bin/configureBioMart.pl line 116. PROXY: LOCATION: biomart You can change the above configuration by editing "biomart-perl/conf/settings.conf" Got usable Apache in /u1/ET/ensembl/ensembl/apache2/bin/httpd, probing for version & ModPerl configuration Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf. Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC Libdir /u1/ET/ensembl/branch-ensembl-45/biomart-perl/lib is not in @INC, adding to @INC Connection parameters of [UNIPROT PROTOTYPE (EBI)] [ OK ] Connection parameters of [MSD PROTOTYPE (EBI)] [ OK ] [NEW CONFIGURATION] .... WITH MEMORY [default] default ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location .......................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence .......................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... UNIPROT PROTOTYPE (EBI) .. 003/006 ... uniprot_cell_component .................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... UNIPROT PROTOTYPE (EBI) .. 004/006 ... uniprot_biol_process ...................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot ................................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... UNIPROT PROTOTYPE (EBI) .. 006/006 ... uniprot_mol_function ...................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd ....................................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6 ... OK Setting possible links between datasets ....(scanning) 100% ....(linking) 100% ....(sorting) 100% ....(clustering) 7/7 ....(resolving) 100% Building templates for visible datasets .... 100% Compiling templates for visible datasets [1/2] Attribute Panel of Dataset.. :uniprot [1/2] Filter Panel of Dataset..... :uniprot [2/2] Attribute Panel of Dataset.. :msd [2/2] Filter Panel of Dataset..... :msd ======================================== this is the content of conf/settings.conf: ######################################################### ################ httpd.conf settings #################### [httpdSettings] #apacheBinary=/usr/sbin/httpd apacheBinary=/u1/ET/ensembl/ensembl/apache2/bin/httpd #serverHost=test.biomart.org serverHost=localhost port=9002 #port=3128 # to use proxying set the proxy port below (even if its 80) and set serverHost as your proxy host #proxy=3128 location=biomart # Colours settings for MARTVIEW # A good online tool help with picking a palette is; # http://slayeroffice.com/tools/color_palette/ [cssSettings] # The default theme, based on a 6-level grey scale from black to white. colour_saturation0=black colour_saturation20=black colour_saturation40=#666666 colour_saturation60=#CCCCCC colour_saturation80=#E5E5E5 colour_saturation100=white # The blue theme used for WormMart #colour_saturation0=black #colour_saturation20=#5870A3 #colour_saturation40=#8294BA #colour_saturation60=#D5DBE8 #colour_saturation80=#EFF1F6 #colour_saturation100=white font_colour_top_bottom_menubar = #000 font_colour_rest = #000 summary_panel_bgcolour = #ffffdd main_panel_bgcolour = #fff top_bottom_menubar_bgcolour = #efefef blocks_outline_colour = #efefef summary_panel_highlight_border_colour = #ffd9af summary_panel_highlight_bgcolour = #ffd9af # These settings relate to the text displayed in the interface drop downs [aliases] Schema=- CHOOSE SCHEMA - Database=- CHOOSE DATABASE - Dataset=- CHOOSE DATASET - # If an attribute URL is specified relatively such as '/geneview/?=%s' # then by default this will be used relative to the current host # However if you set exturl below then this will be prefixed # to these URLs [urlPrefixes] exturl=http://byzvse:1235 # These settings are used to control how the background # results jobs are managed. # # Set resultsDirCount to the number of results directories # you want to use. Then, use resultsDir1, resultsDir2 etc. # to assign names for these directories, up to resultsDirN # where N is the value of resultsDirCount. Background jobs # will be assigned to each of these resultsDir locations # by a hash function which is intended to distribute them # evenly. # # Use resultsDir to specify where # files containing results from background jobs are stored. # This folder must (a) exist and (b) be writable by the # owner of the web server process. # # The enable setting should have a value of 'yes' # if you want background jobs to be available to the user. # Any other value, including non-lowercase versions of 'yes' # will turn background jobs off. [background] resultsDirCount=1 #resultsDir1=/ebi/www/biomart/test/files resultsDir1=/u1/ET/ensembl/ensembl/biomart-results enable=yes # Mail settings are used for informing users when their # background tasks are finished. The mailerType defines # the way in which mail is sent, as understood by # Mail::Mailer. For details of how to control this, see: # # http://search.cpan.org/dist/MailTools/Mail/Mailer.pm # # The from address is the address that messages will # appear to be from. [mailSettings] mailerType=sendmail subject=Your BioMart results are ready [EMAIL PROTECTED] # These settings relate to sessions. # # The expire setting relates to how long sessions will live # on disk for. If not accessed for a period of time longer than # this, then the session will be dropped. Aliases are: # # +-----------+---------------+ # | alias | meaning | # +-----------+---------------+ # | s | Second | # | m | Minute | # | h | Hour | # | d | Day | # | w | Week | # | M | Month | # | y | Year | # +-----------+---------------+ # # Driver could have values based on where you want the session to be # stored. default or no value assigned is set to Berkeley DB implementation. # All possible values could be: # driver= # driver=default # driver=files # driver=mysql # driver=oracle # a database table must already exist with any name but with strict columnName/Types # EXAMPLES # ========== MySQL ============ # first create the table as # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session LONGTEXT NOT NULL ) ; # then the following settings should follow under [sessions] # driver=mysql # dsn=DBI:mysql:database=YOU_DATABASE_NAME;host=127.0.0.1;port=3306 # user=root # pass= # ========== ORACLE ============ # first create the table as # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session CLOB NOT NULL ) ; # then the following settings should follow under [sessions] # driver=oracle # dsn=dbi:Oracle:host=172.22.70.89;sid=XE;port=1521 # user=root # pass= [sessions] expire=12h driver=default # Web Service Logging options [webserviceLogging] mode=ON log_query=ON log_IP=ON ===================================================== biomart-perl/conf/error_log does not exist as I am using the ensembl web server. Here is the relevant part of the ensembl apache2 error log: [Mon Aug 06 18:31:52 2007] [notice] Apache/2.2.4 (Unix) mod_perl/2.0.3 Perl/v5.8.5 configured -- resuming normal operations INIT WEB MODULE... at /u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/PageStub.pm line 27. Use of uninitialized value in concatenation (.) or string at /u1/ET/ensembl/ensembl/biomart-perl/lib/BioMart/Web.pm line 1784\ . INIT WEB MODULE... at /u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/PageStub.pm line 27. These are the relevant lines in Web.pm: my $allAttributeTrees = $registry->getConfigTreeForDataset($dataset_name, $schema_nam\ e, 'default')->getAllAttributeTrees(); my $atttree = $allAttributeTrees->[0]; # first one is supposed to be the default one $logger->debug("Got outputformats ".$atttree." for attpage $attributepage, in dataset\ $dataset_name"); Thanks for your help and Best Regards, Felix Natter _________________________________________ Bayer HealthCare AG BHC-PK Elberfeld, 0500 Phone: Fax: E-mail: [EMAIL PROTECTED] Web: http://www.bayerhealthcare.com Vorstand: Arthur Higgins, Vorsitzender | Werner Baumann, Hartmut Klusik, Lykele van der Broek, Gunnar Riemann Vorsitzender des Aufsichtsrats: Richard Pott Sitz der Gesellschaft: Leverkusen | Eintragung: Amtsgericht Köln, HRB 49894 ================================ Die vorangehende e-mail inkl. jeglicher Anhänge beinhaltet Informationen, die vertraulich oder nicht für die Öffentlichkeit bestimmt sein könnten. Sie ist nur für den/die designierten Empfänger bestimmt. Sollten Sie nicht der designierte Empfänger sein, informieren Sie bitte den Absender und löschen Sie die Nachricht aus Ihrem System. Gebrauch, Verbreitung, Verteilung oder Reproduktion dieser Nachricht sind untersagt und können rechtswidrig sein. ================================ The preceding e-mail message (including any attachments) contains information that may be confidential, or constitute non-public information. It is intended to be conveyed only to the designated recipient(s). If you are not an intended recipient of this message, please notify the sender by replying to this message and then delete it from your system. Use, dissemination, distribution, or reproduction of this message by unintended recipients is not authorized and may be unlawful. Syed Haider <[EMAIL PROTECTED]> Gesendet von: [EMAIL PROTECTED] 03.08.2007 12:00 An [EMAIL PROTECTED] Kopie [email protected] Thema Re: [mart-dev] Problems with biomart 0.6 as part ofensembl Hi Felix could you please forward me - the onscreen response once you execute perl bin/configure.pl -r conf/registryURLPointer.xml --clean - your biomart-perl/conf/settings.conf - conf/error_log and most important of all, have you tried installing biomart independently first and see if it works for you, then we can take a step forward to get this to work with Ensembl. for instructions about how to install biomart independently, follow DOCS tab on www.biomart.org for any further help, free to write back. kind regards syed On Fri, 2007-08-03 at 11:51 +0200, [EMAIL PROTECTED] wrote: > perl bin/configure.pl -r conf/registryURLPointer.xml -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
