Hi Roger,
the httpd.conf you are referring is a default one which contains every
possible directive apache web server supports. I dont see a point
loading all the possible modules with httpd with out having a need to do
so. This httpd.conf, is for help and for copy paste so you can create
your own appropriate httpd.conf. Thats precisely why we generate our own
httpd.conf which is short and concise, loading very modules. As far as
your mod_perl and apxs/2 is concerned, I am pretty sure BioMart doesnt
work with out mod_perl. And if apxs/2 from configureBioMart.pl cannot
find mod_perl, then BioMart's independent installation would not have
worked in the first place. I would recommend you to get the independent
installation to work first. The configure script should be able to find
the right directory of apache modules through apxs/2 -q LIBEXECDIR
command. Please try reinstalling your apxs/2 and it should point to the
module directory which you believe is correct. Just a hint about
mod_perl, when you install it, you can supply a switch which points to
the location of apxs/2
e.g
perl Makefile.PL \
PREFIX=/home/biomart/apache \
MP_APXS=/home/biomart/apache/bin/apxs
hope this helps
syed
On Tue, 2008-01-29 at 22:46 +0000, Roger Hull wrote:
> Hi Seyd,
>
> Thanks again for your quick reply.
>
> I don't know about two different installations of Apache, this was a
> pre-installed (virtual) server, with Apache and Perl set up
> professionally according to the hosting company's standard practices.
> The only things I have installed are biomart-perl, the pre-requisite
> perl modules, and apxs.
>
> mod-perl: I can see the Apache directive:
> LoadModule perl_module modules/mod_perl.so
>
> in the file perl.conf, (which is included in httpd.conf), and I understand
> this to mean load 'mod_perl.so' from the 'modules' subdirectories of the
> Apache ServerRoot, which is '/etc/httpd'.
>
> As I found the file mod_perl.so in the directory /etc/httpd/modules, and
> there were no error messages messages relating to mod_perl in the Apache
> error log, I suppose I do have mod_perl installed.
>
> Do you agree with my interpretation? If so, I guess there must be some other
> cause for the problem that I see with martview than the lack of mod_perl.
>
> --------------
>
> I then wondered why configureBioMart.pl did not indicate that mod_perl was
> installed - I found the option apxs -q LIBEXECDIR in the apxs documentation
> on the Apache site, but I couldn't find on this site any explanation of why
> this should give the location of Apache modules, hence my question. The only
> way I am aware of for locating Apache modules is to look at the LoadModule
> and ServerRoot directives in httpd.conf. Anyway, I leave this to you.
>
> Regards,
> Roger.
> Syed Haider wrote:
> > Hi Roger
> >
> > apxs or apxs2, both should work fine. apxs/2 -q LIBEXECDIR gives you the
> > path to modules directory of the apache with which this apxs/2 is
> > associated. Pardon my knowledge, if you want to investigate if this is
> > the best way to discover this, please consult apxs/2 documentation or
> > apache web server docs. You have two different locations for apache
> > modules and they have several modules in common, which suggests that you
> > have two different installations of apache. The apxs under discussion
> >
> > /usr/sbin/apxs -q LIBEXECDIR
> > /usr/local/psa/admin/libexec
> >
> > gives you the path to modules directory with which this apxs/2 is
> > associated through respective apache.
> >
> > hope this explains the behaviour of apxs/2.
> >
> > regards
> > syed
> >
> >
> >
> >
> > On Tue, 2008-01-29 at 19:44 +0000, Roger Hull wrote:
> >
> > > Hi Syed,
> > >
> > > mod_perl does seem to be installed: perl.conf (in
> > > httpdconf_extra.tar.gz that I sent you) is included by the main
> > > httpd.conf as noted below:
> > > Include conf.d/*.conf
> > >
> > >
> > > You can see the loadmodule directive for mod_perl in perl.conf:
> > >
> > > LoadModule perl_module modules/mod_perl.so
> > >
> > >
> > > I think that configureBioMart.pl does not find mod_perl because the
> > > directory returned by
> > >
> > > /usr/sbin/apxs -q LIBEXECDIR is
> > >
> > > /usr/local/psa/admin/libexec
> > >
> > > which does contain so modules:
> > >
> > > ls /usr/local/psa/admin/libexec
> > > httpd.exp mod_alias.so mod_autoindex.so mod_digest.so
> > > mod_headers.so mod_log_config.so mod_negotiation.so mod_status.so
> > > mod_vhost_alias.so
> > > libproxy.so mod_asis.so mod_cern_meta.so mod_dir.so
> > > mod_imap.so mod_log_forensic.so mod_rewrite.so
> > > mod_unique_id.so
> > > mod_access.so mod_auth.so mod_cgi.so mod_env.so
> > > mod_include.so mod_mime.so mod_setenvif.so
> > > mod_userdir.so
> > > mod_actions.so mod_auth_anon.so mod_define.so mod_expires.so
> > > mod_info.so mod_mime_magic.so mod_speling.so
> > > mod_usertrack.so
> > >
> > > but not mode_perl, whereas mod_perl is in this directory:
> > >
> > > ls /etc/httpd/modules
> > > libphp5.so mod_authn_dbm.so mod_authz_user.so
> > > mod_deflate.so mod_headers.so mod_mem_cache.so
> > > mod_proxy_ftp.so mod_unique_id.so
> > > mod_actions.so mod_authn_default.so mod_autoindex.so
> > > mod_dir.so mod_ident.so mod_mime.so
> > > mod_proxy_http.so mod_userdir.so
> > > mod_alias.so mod_authn_file.so mod_cache.so
> > > mod_disk_cache.so mod_imagemap.so mod_mime_magic.so
> > > mod_python.so mod_usertrack.so
> > > mod_asis.so mod_authnz_ldap.so mod_cern_meta.so
> > > mod_dumpio.so mod_include.so mod_negotiation.so
> > > mod_rewrite.so mod_version.so
> > > mod_auth_basic.so mod_authz_dbm.so mod_cgi.so
> > > mod_env.so mod_info.so mod_perl.so
> > > mod_setenvif.so mod_vhost_alias.so
> > > mod_auth_digest.so mod_authz_default.so mod_cgid.so
> > > mod_expires.so mod_ldap.so mod_proxy.so
> > > mod_speling.so
> > > mod_authn_alias.so mod_authz_groupfile.so mod_dav.so
> > > mod_ext_filter.so mod_log_config.so mod_proxy_ajp.so
> > > mod_ssl.so
> > > mod_authn_anon.so mod_authz_host.so mod_dav_fs.so
> > > mod_file_cache.so mod_log_forensic.so mod_proxy_balancer.so
> > > mod_status.so
> > > mod_authn_dbd.so mod_authz_owner.so mod_dbd.so
> > > mod_filter.so mod_logio.so mod_proxy_connect.so
> > > mod_suexec.so
> > >
> > > and this is the modules directory under ServerRoot, which is where
> > > Apache looks for modules loaded with a relative path.
> > >
> > > ServerRoot "/etc/httpd"
> > >
> > > I have apxs, not apxs2, but this is what Apache 2.2 refers to - see
> > > http://httpd.apache.org/docs/2.2/programs/apxs.html
> > >
> > > but where in the Apache documentation does it say that LIBEXECDIR is
> > > where to find the modules to be loaded?
> > >
> > > Regards,
> > > Roger.
> > >
> > > Syed Haider wrote:
> > >
> > > > 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.
======================================
