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...
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
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