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.
the paths are deliberately like this as all BioMart installation and post-installation (apache, logs etc ) is relative to biomart-perl directory. you should start apache as apache -d biomart-perl/conf and you may use -f to point to biomart-perl/conf/httpd.conf I would suggest you to first get the server running as suggested in docs, and then try moving things to different directories and editing httpd.conf. The latter works too and people do it all the time, but it should be done once you have the system running with naive setup. > 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... > > > > 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. ======================================
