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>
