[ome-users] Problems during OME installation - MOD_PERL is not working properly
Curtis Rueden
ctrueden at wisc.edu
Mon Jan 26 19:01:01 GMT 2009
Hi Arnon,
Sorry for the delay in my reply; I just returned from vacation.
Actually I didn't notice that OME is no longer onder development... thank
> you for mention that.
>
> Our Lab equipped mostly with Zeiss microscopes, controlled by SlideBook
> program. I sow that the OME give a support for the necessary file format
> (*.sld). Also we interested in the option for interface with MATLAB and
> Pyton.
>
The OME Perl server ostensibly supports SlideBook because it can use
Bio-Formats, which supports it, but please note that the OME/Bio-Formats
interface has not been thoroughly tested.
Also we interested in the option for interface with MATLAB and Pyton.
>
OMERO is capable of interfacing with MATLAB and Python code:
http://trac.openmicroscopy.org.uk/omero/wiki/OmeroMatlab
http://trac.openmicroscopy.org.uk/omero/wiki/OmeroPy
Things are fluctuating a bit in preparation for the Beta4.0 release, but
should stabilize soon, including better documentation.
Do the OMERO support the SlideBook format ? Would you recommand using OMERO
> insteed of OME ?
>
Not currently. However, since Bio-Formats supports SlideBook, it is only a
matter of time until OMERO does as well -- probably some time later this
year. The problem with SlideBook is that there is virtually no documentation
available on the format, so we have reverse engineered it, but we cannot
currently make any promises of "metadata completeness" or similar.
Can I install OMERO on the same server where I started to install OME
> without format the whole OS?
>
Yes, no problem.
Would you suggest to wait for the release of the beta version 4.x before
> starting install OMERO?
>
At this point, yes, since Beta4.0 will be out within a month or so, and is a
fairly major shift from Beta3.2.
Thanks a lot for your helpful advises, Arnon.
>
You're welcome.
-Curtis
On Sun, Jan 18, 2009 at 1:43 AM, Kinneret Lab <kinneret.lab at gmail.com>wrote:
> Hi Curtis,
>
> Actually I didn't notice that OME is no longer onder development... thank
> you for mention that.
>
> Our Lab equipped mostly with Zeiss microscopes, controlled by SlideBook
> program. I sow that the OME give a support for
>
> the necessary file format (*.sld). Also we interested in the option for
> interface with MATLAB and Pyton.
>
> Do the OMERO support the SlideBook format ? Would you recommand using OMERO
> insteed of OME ?
>
> Can I install OMERO on the same server where I started to install OME
> without format the whole OS?
>
> Would you suggest to wait for the release of the beta version 4.x before
> starting install OMERO?
>
>
> Thanks a lot for your helpful advises, Arnon.
>
>
> 2009/1/17 Curtis Rueden <ctrueden at wisc.edu>
>
> Hi Arnon,
>>
>> Strange, it does indeed look the mod_perl test is working, so I'm not sure
>> why the installer is failing on that step. IIRC the installer just uses
>> curl, so you could try accessing the URL with curl rather than your web
>> browser.
>>
>> Please note that the OME server 2.x is no longer under active development,
>> and we can only provide limited support. We suggest you try the OMERO
>> server, which is currently under active development and better supported
>> than the legacy OME server. If there is a feature you want that OME 2.x has,
>> that OMERO doesn't have, we are definitely interested in hearing about it!
>>
>> -Curtis
>>
>> On Fri, Jan 16, 2009 at 2:15 AM, Kinneret Lab <kinneret.lab at gmail.com>wrote:
>>
>>> Hi,
>>>
>>>
>>>
>>> I've a problem while installing OME server on centOS 5 at the stage of
>>>
>>>
>>> Apache configuration :
>>>
>>> I get this output during the installation:
>>> -------------------------------------------------------------------------------------------------------------------
>>>
>>> .
>>> .
>>> .
>>> Apache configuration:
>>> Configure Apache?: yes
>>> Developer configuration: no
>>> Server restart?: yes
>>> Install OME servers:
>>> Images (omeis): yes
>>> Data (omeds): yes
>>>
>>>
>>>
>>>
>>> Web: yes
>>> Apache directories:
>>> httpd binary: /usr/sbin/httpd
>>> apachectl binary: /usr/sbin/apachectl
>>> DocumentRoot: /var/www/html
>>> cgi-bin: /var/www/cgi-bin
>>>
>>>
>>>
>>>
>>> Web-UI HTML Templates:
>>> Developer configuration: no
>>>
>>> Are these values correct ? [y/n]:
>>> [Fri Jan 16 09:18:40 2009] [warn] module perl_module is already loaded, skipping
>>> [Fri Jan 16 09:18:40 2009] [warn] The ScriptAlias directive in /OME/conf/httpd2.omeis.conf at line 2 will probably never match because it overlaps an earlier ScriptAlias.
>>>
>>>
>>>
>>>
>>> Testing Apache configuration
>>> \__ mod_perl [FAILURE].
>>>
>>>
>>> Errors executing task: Apache/mod_perl is not properly configured.
>>> Did not get a response from http://localhost/perl2/mod_perl_test.pl.
>>>
>>>
>>>
>>>
>>> See /var/tmp/OME/install/ApacheConfigTask.log for more details. at (eval 187) line 1
>>>
>>> at install.pl line 82
>>> main::run_tasks() called at install.pl line 266
>>> # Looks like your test died before it could output anything.
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------------------------------------------------
>>>
>>> The ApacheConfigTask.log show this:
>>>
>>> Apache setup
>>> Apache binary: /usr/sbin/httpd
>>> apachectl binary: /usr/sbin/apachectl
>>>
>>>
>>>
>>>
>>> httpd root: /etc/httpd
>>> httpd conf: /etc/httpd/conf/httpd.conf
>>> httpd version: 2
>>> Apache configuration:
>>> Configure Apache?: yes
>>> Developer configuration: no
>>> Server restart?: yes
>>> Install OME servers:
>>>
>>>
>>>
>>>
>>> Images (omeis): yes
>>> Data (omeds): yes
>>> Web: yes
>>> Apache directories:
>>> httpd binary: /usr/sbin/httpd
>>> apachectl binary: /usr/sbin/apachectl
>>>
>>>
>>>
>>>
>>> DocumentRoot: /var/www/html
>>> cgi-bin: /var/www/cgi-bin
>>> Web-UI HTML Templates:
>>> Developer configuration: no
>>> Configuring Apache
>>> httpd.conf is /etc/httpd/conf/httpd.conf
>>> Installing OMEIS
>>>
>>>
>>>
>>>
>>> Copying src/C/omeis/omeis to /var/www/cgi-bin/omeis
>>> chmod 0755 /var/www/cgi-bin/omeis
>>> chown /var/www/cgi-bin/omeis to uid: 48 gid: 501
>>> Set APACHE_OMEIS_INCLUDE to Include /OME/conf/httpd2.omeis.conf
>>> Forking a process to upgrade OMEIS
>>>
>>>
>>>
>>>
>>> Installing OMEDS
>>> Set APACHE_OMEDS_INCLUDE to Include /OME/conf/httpd2.omeds.conf
>>> Installing WEB
>>> Copying src/perl2/serve.pl to /OME/perl2/serve.pl
>>> chmod 0755 /OME/perl2/serve.pl
>>> chown /OME/perl2/serve.pl to uid: 48 gid: 501
>>>
>>>
>>>
>>>
>>> Copying src/html/index.html to /var/www/html/index.html
>>> chmod 0644 /var/www/html/index.html
>>> chmod 0644 /var/www/html/favicon.ico
>>> Set APACHE_WEB_INCLUDE to Include /OME/conf/httpd2.web.conf
>>> Installing DAE web by copying NonblockingSlaveWorkerCGI
>>>
>>>
>>>
>>>
>>> Copying src/perl2/OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl to /OME/perl2/NonblockingSlaveWorkerCGI.pl
>>> chmod 0755 /OME/perl2/NonblockingSlaveWorkerCGI.pl
>>> chown /OME/perl2/NonblockingSlaveWorkerCGI.pl to uid: 48 gid: 501
>>>
>>>
>>>
>>>
>>> Installing OME-startup.pl
>>> Copying src/perl2/OME-startup.pl to /OME/conf/OME-startup.pl
>>> chown /OME/conf/OME-startup.pl to uid: 48 gid: 501
>>> Fixing variables in conf/httpd.ome.*.conf
>>> Replacing %OME_DIST_BASE with /home/arnon/Desktop/OME-2.6.1
>>>
>>>
>>>
>>>
>>> Replacing %OME_INSTALL_BASE with /OME
>>> Reading /OME/conf/httpd.ome.conf
>>> Writing /OME/conf/httpd.ome.conf
>>> Reading /OME/conf/httpd.omeds-dev.conf
>>> Writing /OME/conf/httpd.omeds-dev.conf
>>> Reading /OME/conf/httpd.omeds.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd.omeds.conf
>>> Reading /OME/conf/httpd.omeis-dev.conf
>>> Writing /OME/conf/httpd.omeis-dev.conf
>>> Reading /OME/conf/httpd.omeis.conf
>>> Writing /OME/conf/httpd.omeis.conf
>>> Reading /OME/conf/httpd.web-dev.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd.web-dev.conf
>>> Reading /OME/conf/httpd.web.conf
>>> Writing /OME/conf/httpd.web.conf
>>> Reading /OME/conf/httpd1.99.omeds-dev.conf
>>> Writing /OME/conf/httpd1.99.omeds-dev.conf
>>> Reading /OME/conf/httpd1.99.omeds.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd1.99.omeds.conf
>>> Reading /OME/conf/httpd1.99.omeis-dev.conf
>>> Writing /OME/conf/httpd1.99.omeis-dev.conf
>>> Reading /OME/conf/httpd1.99.omeis.conf
>>> Writing /OME/conf/httpd1.99.omeis.conf
>>> Reading /OME/conf/httpd1.99.web-dev.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd1.99.web-dev.conf
>>> Reading /OME/conf/httpd1.99.web.conf
>>> Writing /OME/conf/httpd1.99.web.conf
>>> Reading /OME/conf/httpd2.omeds-dev.conf
>>> Writing /OME/conf/httpd2.omeds-dev.conf
>>> Reading /OME/conf/httpd2.omeds.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd2.omeds.conf
>>> Reading /OME/conf/httpd2.omeis-dev.conf
>>> Writing /OME/conf/httpd2.omeis-dev.conf
>>> Reading /OME/conf/httpd2.omeis.conf
>>> Writing /OME/conf/httpd2.omeis.conf
>>> Reading /OME/conf/httpd2.web-dev.conf
>>>
>>>
>>>
>>>
>>> Writing /OME/conf/httpd2.web-dev.conf
>>> Reading /OME/conf/httpd2.web.conf
>>> Writing /OME/conf/httpd2.web.conf
>>> Reading /OME/conf/httpd.ome.conf
>>> Writing /OME/conf/httpd.ome.conf
>>> Restarting Apache
>>> Executing /usr/sbin/apachectl restart
>>>
>>>
>>>
>>>
>>> Getting an OME::Util::cURL user agent
>>> Generated mod_perl test script:
>>> #!/usr/bin/perl -w
>>> use strict;
>>> use CGI qw/-no_xhtml/;
>>>
>>> my $CGI = CGI->new();
>>> print $CGI->header(-type => 'text/plain'),
>>>
>>>
>>>
>>>
>>>
>>> my ($key,$value);
>>> while ( ($key, $value) = each %ENV)
>>> {
>>> print "$key = $value\n";
>>> }
>>>
>>>
>>> 1;
>>>
>>> Writing script to /OME/perl2/mod_perl_test.pl
>>> Getting response from http://localhost/perl2/mod_perl_test.pl
>>>
>>>
>>>
>>>
>>> Apache/mod_perl is not properly configured. Did not get a response from http://localhost/perl2/mod_perl_test.pl.
>>>
>>> -----------------------------------------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> When I access the file directly in my web browser "http://localhost/perl2/mod_perl_test.pl"
>>> , this is the output I get:
>>>
>>> SCRIPT_NAME = /perl2/mod_perl_test.pl
>>>
>>>
>>>
>>>
>>> SERVER_NAME = localhost
>>> SERVER_ADMIN = root at localhost
>>> HTTP_ACCEPT_ENCODING = gzip,deflate
>>> HTTP_CONNECTION = keep-alive
>>> REQUEST_METHOD = GET
>>> HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
>>>
>>>
>>>
>>>
>>> SCRIPT_FILENAME = /OME/perl2/mod_perl_test.pl
>>> SERVER_SOFTWARE = Apache/2.2.3 (CentOS)
>>> HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7
>>> QUERY_STRING =
>>> REMOTE_PORT = 39160
>>> HTTP_USER_AGENT = Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.5) Gecko/2008121911 CentOS/3.0.5-1.el5.centos Firefox/3.0.5
>>>
>>>
>>>
>>>
>>> SERVER_PORT = 80
>>> SERVER_SIGNATURE = <address>Apache/2.2.3 (CentOS) Server at localhost Port 80</address>
>>>
>>> HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5
>>> REMOTE_ADDR = 127.0.0.1
>>> HTTP_KEEP_ALIVE = 300
>>>
>>>
>>>
>>> SERVER_PROTOCOL = HTTP/1.1
>>>
>>> MOD_PERL_API_VERSION = 2
>>> PATH = /usr/bin/:/usr/local/bin/:/sw/bin/
>>> REQUEST_URI = /perl2/mod_perl_test.pl
>>> GATEWAY_INTERFACE = CGI/1.1
>>> SERVER_ADDR = 127.0.0.1
>>> DOCUMENT_ROOT = /var/www/html
>>> HTTP_HOST = localhost
>>>
>>>
>>>
>>>
>>> MOD_PERL = mod_perl/2.0.2
>>> -----------------------------------------------------------------------------------------------------------------------
>>>
>>> I guess it means that the script works well ...right ? so I'm not sure what is the problem...
>>>
>>>
>>>
>>>
>>> Could someone please assist me in resolving this problem
>>>
>>>
>>>
>>> Thanks in advance, Arnon.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
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