Glad to hear that all works now. When your deployment is finished,
please let us know, we are happy to link it and add it to BioMart
Central Portal (www.biomart.org).
Cheers
Syed
[email protected] wrote:
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.
======================================
