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. > > > > > > > > > > > > > > > > > > > > >
