Hi Syed and other friends,
the mart works! (http://mandolin.caltech.edu:5430/biomart/martview)
Thank you very much!!
Dong
> Hi Dong,
>
> Apache seems to be unhappy :) the user directive you have added to
> httpd.conf does not have the right permissions on the biomart-perl/
> directory. A good test would be to
>
> chmod -R 775 biomart-perl
>
> and see if that fixes the problem.
>
> Good luck!
> Syed
>
>
>> Hi Syed,
>>
>> Thank you very much!! this problem seems solved, however, there is
>> another
>> problem showing up, could you help me again? error_log says:
>>
>> [error] Error in processing template error.tt: file error - cache
>> failed
>> to write error.ttc: Error in tempfile() using /var/www/ht
>> ml/biomart-perl/conf/templates/default/XXXXXXXXXX: Parent directory
>> (/var/www/html/biomart-perl/conf/templates/default/) is not writable\n
>> at
>> /usr/lib/perl5/
>> site_perl/5.8.8/i386-linux-thread-multi/Template/Document.pm line
>> 295\n\n\nTrace begun at /var/www/html/biomart-perl/lib/BioMart/Web.pm
>> line
>> 267\nBioMart::We
>> b::process_template('BioMart::Web=HASH(0x81ec2e0c)', 'error.tt',
>> 'HASH(0x84383194)') called at
>> /var/www/html/biomart-perl/cgi-bin/martview
>> line 122\nModPerl:
>> :ROOT::ModPerl::Registry::var_www_html_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x8421355c)')
>> called at /usr/lib/perl5/vendor_p
>> erl/5.8.8/i386-linux-thread-multi/ModPerl/RegistryCooker.pm line
>> 203\neval
>> {...} at
>> /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/ModPerl/Registry
>> Cooker.pm line
>> 203\nModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x84213610)')
>> called at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Mod
>> Perl/RegistryCooker.pm line
>> 169\nModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x84213610)')
>> called at /usr/lib/perl5/vendor_perl/5.8.8/i3
>> 86-linux-thread-multi/ModPerl/Registry.pm line
>> 30\nModPerl::Registry::handler('ModPerl::Registry',
>> 'Apache2::RequestRec=SCALAR(0x8421355c)') called at -e lin
>> e 0\neval {...} at -e line 0\n
>>
>> Dong
>>
>>> Hi Dong,
>>>
>>> the --clean option is a perl bin/configure.pl switch e.g
>>> perl bin/configure.pl -r conf/your_reg.xml --clean
>>> see docs for details.
>>>
>>> it seems that your httpd.conf needs a apache user directive, the user
>>> who has rights to start/stop apache. please manually add this to
>>> conf/httpd.conf and then start your apache. This is most likely the
>>> case.
>>>
>>> cheers
>>> Syed
>>>
>>>
>>> [email protected] wrote:
>>>> Hi Richard,
>>>>
>>>> could you let me know how to use --clean option in detail? I checked
>>>> the
>>>> error_log which says:
>>>>
>>>> [warn] pid file /var/www/html/biomart-perl/logs/httpd.pid overwritten
>>>> --
>>>> Unclean shutdown of previous Apache run?
>>>> [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user
>>>> name
>>>> from uid 4294967295, you probably need to modify the User directive
>>>> [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user
>>>> name
>>>> from uid 4294967295, you probably need to modify the User directive
>>>> [Tue Jan 13 15:55:44 2009] [notice] Apache/2.2.6 (Unix) mod_perl/2.0.2
>>>> Perl/v5.8.8 configured -- resuming normal operations
>>>> [Tue Jan 13 15:55:44 2009] [alert] Child 24664 returned a Fatal
>>>> error...
>>>> Apache is exiting!
>>>>
>>>> do you have any idea from this information?
>>>>
>>>> Thanks!
>>>>
>>>> Dong
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Also it might be worth checking the contents of the conf/httpd.conf
>>>>> file
>>>>> to see if it has correctly populated it with the correct port numbers
>>>>> etc.
>>>>>
>>>>> If it hasn't, rerun bin/configure.pl with the --clean option to force
>>>>> it
>>>>> to regenerate httpd.conf properly.
>>>>>
>>>>> cheers,
>>>>> Richard
>>>>>
>>>>> [email protected] wrote:
>>>>>
>>>>>> Hi Syed,
>>>>>>
>>>>>> Actually, the host name 'mandolin.caltech.edu' is already in the
>>>>>> /etc/hosts file and the web server works well. I follow your
>>>>>> suggestion
>>>>>> to
>>>>>> try 127.0.0.1, the same trouble happened. could you give me other
>>>>>> suggestion?
>>>>>> Thank you!
>>>>>>
>>>>>> Dong
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Dong,
>>>>>>>
>>>>>>> your apache startup error says it all, the apache server doesnt
>>>>>>> recognise your host name (the one which you are specifying in
>>>>>>> settings.conf). You need to modify the /etc/hosts file on your
>>>>>>> system
>>>>>>> and then restart apache server. Once done, reconfigure BioMart
>>>>>>> (only
>>>>>>> perl bin/configure.pl....) and restart your apache. A good test
>>>>>>> would
>>>>>>> be to put 127.0.0.1 in settings.conf and configure Biomart, restart
>>>>>>> apache and see if you can access the webserver on
>>>>>>> http://127.0.0.1:5430/biomart/martview
>>>>>>>
>>>>>>> Stepwise solution can be seen here:
>>>>>>>
>>>>>>> http://digitaldeviation.com/articles/apache-articles/apache-error-could-not-reliably-determine-servers-fully-qualified-domain-na
>>>>>>>
>>>>>>> Good Luck!,
>>>>>>> Syed
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [email protected] wrote:
>>>>>>>
>>>>>>>> Hi Syed,
>>>>>>>>
>>>>>>>> here is the output after configure:
>>>>>>>>
>>>>>>>> # perl bin/configure.pl -r conf/spbase_annotation1022_6.xml
>>>>>>>>
>>>>>>>> Do you want to install in API only mode [y/n] [n]: n
>>>>>>>>
>>>>>>>> Checking prerequisites ...[Looks good]
>>>>>>>>
>>>>>>>> APACHE: /usr/sbin/httpd
>>>>>>>> HOST: http://mandolin.caltech.edu
>>>>>>>> PORT: 5430
>>>>>>>> PROXY:
>>>>>>>> LOCATION: biomart
>>>>>>>>
>>>>>>>> You can change the above configuration by editing
>>>>>>>> "biomart-perl/conf/settings.conf"
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Got usable Apache in /usr/sbin/httpd, probing for version &
>>>>>>>> ModPerl
>>>>>>>> configuration
>>>>>>>> Have Apache DSO-support and ModPerl library file present,
>>>>>>>> configuring
>>>>>>>> ModPerl in httpd.conf.
>>>>>>>> Libdir /var/www/html/biomart-perl/lib is not in @INC, adding to
>>>>>>>> @INC
>>>>>>>>
>>>>>>>> Processing Cached Registry:
>>>>>>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached
>>>>>>>>
>>>>>>>> # /usr/sbin/httpd -d $PWD -f $PWD/conf/httpd.conf
>>>>>>>>
>>>>>>>> Processing Cached Registry:
>>>>>>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached
>>>>>>>>
>>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>>> line
>>>>>>>> 131.
>>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>>> line
>>>>>>>> 139.
>>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>>> line
>>>>>>>> 158.
>>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>>> line
>>>>>>>> 169.
>>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>>> line
>>>>>>>> 185.
>>>>>>>> httpd: Could not reliably determine the server's fully qualified
>>>>>>>> domain
>>>>>>>> name, using mandolin.caltech.edu for ServerName
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> attached are the httpd.conf and settings.conf.
>>>>>>>>
>>>>>>>> Thank you very much for your help!
>>>>>>>>
>>>>>>>> Dong
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Dong,
>>>>>>>>>
>>>>>>>>> please send me the following:
>>>>>>>>>
>>>>>>>>> - conf/httpd.conf
>>>>>>>>> - on screen output when you run perl bin/configure.pl......
>>>>>>>>> - conf/settings.conf
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> thanks
>>>>>>>>> Syed
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> [email protected] wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi Friends:
>>>>>>>>>>
>>>>>>>>>> I successfully set up a mart in one of my machines, then, I
>>>>>>>>>> moved
>>>>>>>>>> whole
>>>>>>>>>> mart database into another machine, and the configuring ("perl
>>>>>>>>>> bin/configure.pl -r conf/annotation1022_6.xml", "/usr/sbin/httpd
>>>>>>>>>> -d
>>>>>>>>>> $PWD
>>>>>>>>>> -f $PWD/conf/httpd.conf")seems work, however, when point web
>>>>>>>>>> browser
>>>>>>>>>> to
>>>>>>>>>> the corresponding URL, I got a error: "Firefox can't establish a
>>>>>>>>>> connection to the server at mandolin.caltech.edu:5430." does
>>>>>>>>>> this
>>>>>>>>>> mean
>>>>>>>>>> mart is not portable? do I have to build mart at each machine
>>>>>>>>>> separately?
>>>>>>>>>> or I missed some httpd configuration?
>>>>>>>>>> Thanks!
>>>>>>>>>>
>>>>>>>>>> Dong
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>>> Richard Holland, BSc MBCS
>>>>> Finance Director, Eagle Genomics Ltd
>>>>> M: +44 7500 438846 | E: [email protected]
>>>>> http://www.eaglegenomics.com/
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
>
>
> ======================================
> Syed Haider.
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> ======================================
>
>
