Hi Renato, your apache is without mod_perl, get the mod_perl first. 'How to' is described in docs.
An evidence of mod_perl if found will be displayed on screen during configure step (perl bin/configure.pl -r conf.....) and mod_perl directives can be seen in httpd.conf too. In addition, this > Invalid command 'DirectoryIndex', perhaps misspelled or defined by a > module not included in the server configuration is an apache error which is due to missing apache module 'mod_dir.so'. A guide to which apache module is required w.r.t such excpetions, please see this page http://www.netadmintools.com/art398.html syed On Mon, 2008-05-19 at 16:14 +0100, Renato Golin wrote: > Syed Haider wrote: > > there is something wrong with your configuration, do the following: > > > > perl bin/configure.pl -r conf/your_reg.xml --clean > > from the biomart-perl directory. > > Hy Syed, > > > Done. Below are the output, the error when running Apache2 and the > httpd.conf. > > > > ==================== Reconfigure: > > $ 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] > Use of uninitialized value in string ne at > /home/renato/workspace/biomart-perl/bin/configureBioMart.pl line 110. > Use of uninitialized value in regexp compilation at > /home/renato/workspace/biomart-perl/bin/configureBioMart.pl line 112. > > rm /home/renato/workspace/biomart-perl/conf/templates/default/*.ttc > APACHE: /usr/sbin/apache2 > HOST: sbornia.homelinux.net > PORT: 9002 > PROXY: > LOCATION: biomart > > You can change the above configuration by editing > "biomart-perl/conf/settings.conf" > > > > Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl > configuration > Libdir /home/renato/workspace/biomart-perl/lib is not in @INC, adding to > @INC > > Connection parameters of [MSD PROTOTYPE (EBI)] [ OK ] > Connection parameters of [UNIPROT PROTOTYPE (EBI)] [ OK ] > > > > > [NEW CONFIGURATION] .... WITH MEMORY [default] > default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd > ....................................... (WEB) www.biomart.org:80 > ............ -> upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location > .......................... (WEB) www.biomart.org:80 ............ -> > upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence > .......................... (WEB) www.biomart.org:80 ............ -> > upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 003/006 ... > uniprot_cell_component .................... (WEB) www.biomart.org:80 > ............ -> upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 004/006 ... uniprot_biol_process > ...................... (WEB) www.biomart.org:80 ............ -> > upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot > ................................... (WEB) www.biomart.org:80 > ............ -> upgrading to 0.6/0.7 ... OK > default ... UNIPROT PROTOTYPE (EBI) .. 006/006 ... uniprot_mol_function > ...................... (WEB) www.biomart.org:80 ............ -> > upgrading to 0.6/0.7 ... 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.. :msd > [1/2] Filter Panel of Dataset..... :msd > [2/2] Attribute Panel of Dataset.. :uniprot > [2/2] Filter Panel of Dataset..... :uniprot > > > ==================== Running Apache: > > $ apache2 -d conf -f httpd.conf > Syntax error on line 14 of conf/httpd.conf: > Invalid command 'DirectoryIndex', perhaps misspelled or defined by a > module not included in the server configuration > > -- Probably because by running stand-alone, none of the modules were > loaded... Not even the default Apache configuration works this way. > > > -- "-f httpd.conf" because it gets relative to serverroot (-d). > > > > > Also send me your conf/httpd.conf. mart-dev doesnt accept attachments. > > ==================== httpd.conf: > > > PidFile logs/httpd.pid > Timeout 300 > KeepAlive On > MaxKeepAliveRequests 100 > KeepAliveTimeout 15 > MinSpareServers 2 > MaxSpareServers 2 > StartServers 2 > MaxClients 30 > MaxRequestsPerChild 4000 > Listen 9002 > > DirectoryIndex index.html > > TypesConfig conf/mime.types > DefaultType text/plain > AddType image/gif .gif > AddType image/png .png > AddType image/jpeg .jpg .jpeg > AddType text/css .css > AddType text/html .html .htm > AddType text/xml .xml > AddType text/plain .asc .txt > AddType application/pdf .pdf > AddType application/x-gzip .gz .tgz > AddType application/vnd.ms-excel .xls > > ErrorLog logs/error_log > LogLevel warn > LogFormat "%h %l %u %t \"%r\" %>s %b" combined > CustomLog logs/access_log combined > > DocumentRoot "/home/renato/workspace/biomart-perl/htdocs" > <Location /> > Options Indexes FollowSymLinks MultiViews > AllowOverride None > Order allow,deny > Allow from all > </Location> > > ScriptAlias /biomart/martview > "/home/renato/workspace/biomart-perl/cgi-bin/martview" > <Location /biomart/martview> > > AllowOverride None > Options None > Order allow,deny > Allow from all > > <IfModule mod_deflate.c> > ## zip both input and output > SetOutputFilter DEFLATE > SetInputFilter DEFLATE > ## donot zip already zipped files > SetEnvIfNoCase Request_URI > \.(?:exe|t?gz|zip|bz2|sit|rar)$ no-gzip dont-vary > </IfModule> > > Options +ExecCGI > </Location> > > ScriptAlias /biomart/martservice > "/home/renato/workspace/biomart-perl/cgi-bin/martservice" > <Location /biomart/martservice> > AllowOverride None > Options None > Order allow,deny > Allow from all > > Options +ExecCGI > </Location> > > ScriptAlias /biomart/martresults > "/home/renato/workspace/biomart-perl/cgi-bin/martresults" > <Location /biomart/martresults> > AllowOverride None > Options None > Order allow,deny > Allow from all > > Options +ExecCGI > </Location> > > ScriptAlias /biomart/das/dsn > "/home/renato/workspace/biomart-perl/cgi-bin/dsn" > <Location /biomart/das/dsn> > AllowOverride None > Options None > Order allow,deny > Allow from all > > Options +ExecCGI > </Location> -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
