Hi Renato On Mon, 2008-05-19 at 14:04 +0100, Renato Golin wrote: > Ok, got the httpd.conf by symlinking /usr/bin/apxs2 to /usr/sbin. > > Now, the httpd.conf has some problems... > > Please don't take the report below as a critic, I'm actually trying to > understand how to set everything up and those problems below can happen > to anyone outside the project (especially newcomers like me). > > > 1st. Paths > > It uses relative paths as log, pid file and mime types, so it depends > from where I start it. > > I had to put my biomart-perl path before it, but you could have used the > structure directly (as was probably the intention) with the path there > was in the configuration and used all over in the same httpd.conf. > > I was expecting that it would install in a directory that could be > easily accessed by the Apache user, not me. > > As a note only, "AllowOverride none" generates the warning: "Useless use > of AllowOverride" on apache 2.0
> 2nd. Welcome note > > Once I got it running I couldn't tell exactly where were the systems... > When I redirected my browser to: > > http://localhost/biomart/ > > I got a directory listing with /mview/ on it and a help.html inside with > very limited help on it. It'd be good to have an index.html on it that > says something like: > > "Congratulations, you got your biomart running. Now [click here] for > martview, [there] for martservice, ..., and [here] for additional help" > > > 3rd. MartView > > http://localhost/biomart/martview > Shows me the error: > > "ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method > "settingsParams" on an undefined value at > /home/renato/workspace/biomart-perl/lib/BioMart/Web.pm line 128. > > If you repeatedly get directed to this error page, there may be a > problem with your current session parameters. To clear your session and > start with a clean slate, please click the New button below. > > Stacktrace: > Exception::Class::Base::new > /home/renato/workspace/biomart-perl/cgi-bin/martview:101" > > Note: There was no "New" button... > 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. and unless you have this running (martview), no point testing the rest of the system e.g martservice, DAS etc etc. Also send me your conf/httpd.conf. mart-dev doesnt accept attachments. cheers syed > > 4th. MartService > > http://localhost/biomart/martservice > > Returns 500 (Internal Server Error) because the module Log4perl is not > on @INC. My CVS dir /lib is on libpath but there is only one directory > inside it, BioMart. I guess the installation script didn't get this as a > required module... > > When I finally installed Log4perl I got another error: > > cannot create regular file > `/home/renato/workspace/biomart-perl/conf/registry_DOM_XML' : Permission > denied > > That's because Apache run as 'httpd' user and the installation directory > is in my home directory. You should use either the Linux Standard Base > or another directory accessible (RW) by the Apache user. > > Finally I gave FULL access to anyone write on /conf dir and the result > was a plain text HTML source on my browser. > > > > 5th. MartResults > > http://localhost/biomart/martresults > > Returns 500 (Internal Server Error) because of a similar problem as > MartView: > > "Can't call method "settingsParams" on an undefined value at > /home/renato/workspace/biomart-perl/cgi-bin/martresults line 57." > > > > 6th. BioDAS > > http://localhost/biomart/das/dsn > > Returns 500 (Internal Server Error) because: > > Can't locate BioMart/Exception.pm in @INC (@INC contains: /etc/perl > /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 > /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 > /usr/local/lib/site_perl /usr/local/lib/perl/5.8.7 > /usr/local/share/perl/5.8.7 .) at > /home/renato/workspace/biomart-perl/cgi-bin/dsn line 33. > > (ie. biomart-perl/lib is not on @INC). > > > cheers, > --renato > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
