Hi Roger,
Before we further this, you do not have mod_perl. Get mod_perl.so for
your apache. Once done, you will witness its presence right after the
following onscreen message when you run configure script.
Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
configuration
In addition, the corresponding 'LoadModule' statement will be added to
httpd.conf which BioMart generates. BioMart does not work with out
mod_perl.
let me know if it resolves your problem.
cheers
syed
On Tue, 2008-01-29 at 15:10 +0000, Roger Hull wrote:
> Hi Syed,
>
> My comments below your questions. I will send the files you request
> directly to you,
>
> Regards,
> Roger.
>
> Syed Haider wrote:
> > Hi Roger
> > as far as specific version of PERL modules is concerned, they should all
> > work except Time::HiRes if thats not already in your perl. Avoid using
> > the latest one.
> >
> > after cvs co biomart-perl
> >
> > do you run perl bin/configure.pl ... from biomart-perl directory ?
> >
> Of course, as instructed in 'BioMart 0.6 Documentation'. I copy/paste
> the line from the manual, changing only the name of the registry
> file.
> > send me the onscreen response when you run this script.
> >
> Sent separately.
> > please send me your conf/settings.conf, conf/httpd.conf,
> > cgi-bin/martview
> >
> Sent separately.
> > whats the command you use to run apache server, and which directory do
> > you run it from?
> >
> I normally start Apache from Plesk (server management utility), but I
> get the same effect loading the martview page if I start it like this
> in /home/biomart-perl:
> /usr/sbin/httpd -d /etc/httpd/conf
> -f /etc/httpd/conf/httpd.conf
> [Tue Jan 29 14:25:56 2008] [warn] Useless use of AllowOverride
> in line 592.
> [Tue Jan 29 14:25:56 2008] [warn] Useless use of AllowOverride
> in line 610.
> [Tue Jan 29 14:25:56 2008] [warn] Useless use of AllowOverride
> in line 620.
> [Tue Jan 29 14:25:56 2008] [warn] Useless use of AllowOverride
> in line 630.
> [Tue Jan 29 14:25:56 2008] [warn] Useless use of AllowOverride
> in line 640.
> In the above httpd.conf, the following lines are to be found, which
> includes the files in the conf.d directory in alphabetical order. I
> have also sent those to you along with the httpd.conf used to start
> Apache.
> # Load config files from the config directory
> "/etc/httpd/conf.d".
> #
> Include conf.d/*.conf
> > thanks
> > syed
> >
> >
> > On Mon, 2008-01-28 at 23:27 +0000, Roger Hull wrote:
> >
> > > Hi Syed,
> > >
> > > Thanks for the quick response. I still have some comments/questions
> > > about the Apache configuration, but I'll raise those in another thread
> > > (as that doesn't seem to be causing me a problem).
> > >
> > >
> > > > could you first try neat and independent installation of BioMart.
> > > >
> > > I should have said, I already did this after I found problems. I
> > > created a new empty directory and reinstalled everything from scratch
> > > - same results.
> > >
> > > > Also please run the configure script i-e
> > > > (biomart-perl$ perl bin/configure.pl -r conf/reg.xml --clean ), then
> > > > kill/restart your server.
> > > >
> > > And I did this a number of times!
> > >
> > >
> > > > > Should this .cached file exist in the conf directory?
> > > > >
> > > > no, it should reside under conf/cachedRegistries/
> > > >
> > > So there is a problem here, Web.pm is looking for it in the conf
> > > directory, as I said below. But why? (My hack to copy the .cached file
> > > into conf/ was only to try to get to the next step, I would like to go
> > > back and get this working without hacks.)
> > >
> > >
> > > > As you see TAG_path's value is missing and you are already familiar
> > > >
> > > with the code, you can manually stitch it in main.tt and see if
> > > everything works fine.
> > > I'm not so familiar with the code, I just looked to see the immediate
> > > cause of the problem. But I don't think hacking main.tt would get me
> > > far, this problem seems to be more far reaching.
> > >
> > > Also, this test installation will be a guide for a future real
> > > installation, so I would like to get to the bottom of these problems.
> > > Is there any further information I could send you - for example, would
> > > it help to run this with log4perl logging set to debug?
> > >
> > > Are there any perl modules for which it is critical to install the
> > > exact version, rather than the latest version - and might be relevant
> > > to such issues (I guess not, or someone else would have hit the same
> > > problem).
> > >
> > > By the way, the '#!perl -w' vs '#!/usr/bin/perl -w' shebangs caused me
> > > some head scratching at first, martview just gave a blank browser
> > > window, with no clue in the Apache log. It was only when I installed a
> > > test perl script, which worked, that I realised that the shebang was
> > > the cause of this.
> > >
> > > Regards,
> > > Roger
> > >
> > > Syed Haider wrote:
> > >
> > > > Hi Roger,
> > > >
> > > > On Mon, 2008-01-28 at 18:48 +0000, Roger Hull wrote:
> > > >
> > > >
> > > > > Hi,
> > > > > I have been trying to install biomart to run martview and martservice,
> > > > > using an external biomart as the data source. The purpose is to test
> > > > > out customising the biomart web interface. I hit two problems as
> > > > > described below. I'll try to give full details of what I did.
> > > > > uname -a gives Linux <hostname> 2.6.9-023stab046.2-enterprise #1 SMP
> > > > > Mon Dec 10 15:22:33 MSK 2007 i686 i686 i386 GNU/Linux.
> > > > > perl -v gives This is perl, v5.8.8 built for i386-linux-thread-multi
> > > > > I loaded the latest versions of the perl modules required by biomart
> > > > > from CPAN.
> > > > >
> > > > > After installing biomart-perl, I changed conf/settings.conf to:
> > > > > [httpdSettings]
> > > > > apacheBinary=/usr/sbin/httpd
> > > > > serverHost=localHost
> > > > > port=80
> > > > > # to use proxying set the proxy port below (even if its 80)
> > > > > and set serverHost as your proxy host
> > > > > proxy=
> > > > > location=biomart
> > > > > I also changed !#perl -w to !#/usr/bin/perl -w in any scripts that I
> > > > > found the former.
> > > > >
> > > > > I ran perl bin/configure.pl -r conf/registryDBPointer.xml, using the
> > > > > central registry xml file as installed, and it seemed to be
> > > > > successful, ending with "Building templates for visible datasets..."
> > > > >
> > > > > Problem 1: Apache (Apache/2.2.2) does not like the generated
> > > > > htttp.conf - httpd reports:
> > > > > Syntax error on line 14 of /home/biomart/biomart-perl/conf/httpd.conf:
> > > > > Invalid command 'DirectoryIndex', perhaps misspelled or defined by a
> > > > > module not included in the server configuration
> > > > >
> > > > >
> > > > this means apache module mod_dir.so is missing from apache modules
> > > > directory, add it and this message will vanish away.
> > > >
> > > >
> > > >
> > > >
> > > > > The httpd.conf generated looks OK - it starts:
> > > > >
> > > > > PidFile logs/httpd.pid
> > > > > Timeout 300
> > > > > KeepAlive On
> > > > > MaxKeepAliveRequests 100
> > > > > KeepAliveTimeout 15
> > > > > MinSpareServers 2
> > > > > MaxSpareServers 2
> > > > > StartServers 2
> > > > > MaxClients 50
> > > > > MaxRequestsPerChild 0
> > > > > Listen 80
> > > > >
> > > > > DirectoryIndex index.html
> > > > >
> > > > > Anyway, I took the lines from the generated httpd.conf and amalgamated
> > > > > them into the previous (working) httpd.conf. Now the server starts up
> > > > > and I can see, for example, http://<my server>/index.html as the
> > > > > introductory biomart page.
> > > > > I also added a small perl test script in cgi-bin, and this ran OK from
> > > > > my browser.
> > > > > (In my opinion this method of giving a completely new httpd.conf is
> > > > > anyway not very convenient if someone wants to run other services than
> > > > > martview on their server).
> > > > >
> > > > >
> > > > It is possible to merge our directives into other httpd.conf files, but
> > > > i guess adding it automatically to an existing file is'nt safe. We
> > > > provide a simple/basic httpd.conf which is expected to work anywhere.
> > > >
> > > >
> > > >
> > > > > Problem 2: When I loaded the page http://<my server>/biomart/martview
> > > > > from a browser, I got
> > > > > ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
> > > > > "settingsParams" on an undefined value
> > > > > at /home/biomart/biomart-perl/lib/BioMart/Web.pm line 118.
> > > > >
> > > > > line 118: my $mart_registry = $self->get_mart_registry();
> > > > > and get_mart_registry: return $self->get('mart_registry');
> > > > > and 'mart_registry' doesn't seem to be in the hash, so we get null.
> > > > > This seems to be caused by Web.pm looking for
> > > > > conf/registryDBPointer.xml.cached, which does not exist. Web.pm
> > > > > doesn't seem to handle properly the case that the file doesn't exist,
> > > > > only the case that it fails to deserialise correctly.
> > > > > (By the way, in cgi-bin/martview, I have $CONF_FILE =
> > > > > '/home/biomart/biomart-perl/conf/registryDBPointer.xml';)
> > > > >
> > > > > Should this .cached file exist in the conf directory?
> > > > >
> > > > >
> > > > no, it should reside under conf/cachedRegistries/
> > > >
> > > >
> > > >
> > > > > Just to move things forward, I tried copying
> > > > > registryDBPointer.xml.cached from conf/cachedRegistries/ (where there
> > > > > was such a file) to conf/. Now http://<my
> > > > > server>/biomart/martviewgives a page that looks like it's trying to be
> > > > > martview! But just some plain text, like "New Count Results". Looking
> > > > > at the page source I can see why: I have things like
> > > > > <link rel="stylesheet" type="text/css" href="//mview/martview.css" />
> > > > > <script src="//mview/js/martview.js" type="text/javascript"
> > > > > ></script>
> > > > >
> > > > > where the 'location', biomart, is missing from between the double
> > > > > forward slashes. Looks like the TAG_path tag did not get filled in
> > > > > the Template main.tt for some reason.
> > > > >
> > > > >
> > > > could you first try neat and independent installation of BioMart. This
> > > > would identify platform conflicts if there are any. As you see
> > > > TAG_path's value is missing and you are already familiar with the code,
> > > > you can manually stitch it in main.tt and see if everything works fine.
> > > > Also please run the configure script i-e
> > > > (biomart-perl$ perl bin/configure.pl -r conf/reg.xml --clean )
> > > > each time you edit settings.conf or stylesheets, and then kill/restart
> > > > your server.
> > > >
> > > > regards
> > > > syed
> > > >
> > > >
> > > >
> > > > > Your help would be appreciated,
> > > > > Roger.
> > > > >
> > > > >
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
