Hi Arnon,<br><br>Sorry for the delay in my reply; I just returned from vacation.<br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">Actually I didn't notice that OME is no longer onder development... thank you for mention that.<br><br>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. <br>
</div></blockquote><div><br>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.<br><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Also we interested in the option for interface with
MATLAB and Pyton. <br></div></blockquote><br>
OMERO is capable of interfacing with MATLAB and Python code:<br><a href="http://trac.openmicroscopy.org.uk/omero/wiki/OmeroMatlab">http://trac.openmicroscopy.org.uk/omero/wiki/OmeroMatlab</a><br><a href="http://trac.openmicroscopy.org.uk/omero/wiki/OmeroPy">http://trac.openmicroscopy.org.uk/omero/wiki/OmeroPy</a><br>
<br>Things are fluctuating a bit in preparation for the Beta4.0 release, but should stabilize soon, including better documentation.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">Do the OMERO support the SlideBook format ? Would you recommand using OMERO insteed of OME ?<br></div></blockquote><div><br>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.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Can I install OMERO on the same server where I started to install OME without format the whole OS?<br>
</div></blockquote><div><br>Yes, no problem.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Would you suggest to wait for the release of the beta version 4.x before starting install OMERO?</div>
</blockquote><div><br>At this point, yes, since Beta4.0 will be out within a month or so, and is a fairly major shift from Beta3.2.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">Thanks a lot for your helpful advises, Arnon. <br></div></blockquote></div><br>You're welcome.<br><br>-Curtis<br><br><div class="gmail_quote">On Sun, Jan 18, 2009 at 1:43 AM, Kinneret Lab <span dir="ltr"><<a href="mailto:kinneret.lab@gmail.com">kinneret.lab@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Hi Curtis, <br><br>Actually I didn't notice that OME is no longer onder development... thank you for mention that.<br>
<br>Our Lab equipped mostly with Zeiss microscopes, controlled by SlideBook program. I sow that the OME give a support for <br>
<br>the necessary file format (*.sld). Also we interested in the option for interface with MATLAB and Pyton. <br><br>Do the OMERO support the SlideBook format ? Would you recommand using OMERO insteed of OME ?<br><br>Can I install OMERO on the same server where I started to install OME without format the whole OS?<br>
<br>Would you suggest to wait for the release of the beta version 4.x before starting install OMERO?<br><br><br>Thanks a lot for your helpful advises, Arnon. <br><br><br><div class="gmail_quote">2009/1/17 Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span><div>
<div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); border-right: 1px solid rgb(204, 204, 204); margin: 0pt 0.8ex; padding-left: 1ex; padding-right: 1ex;">Hi Arnon,<br><br>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.<br>
<br>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!<br>
<font color="#888888">
<br>-Curtis<br><br></font><div class="gmail_quote"><div><div></div><div>On Fri, Jan 16, 2009 at 2:15 AM, Kinneret Lab <span dir="ltr"><<a href="mailto:kinneret.lab@gmail.com" target="_blank">kinneret.lab@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div><div dir="rtl"><div dir="ltr"><pre>Hi,<br><br>
<br>I've a problem while installing OME server on centOS 5 at the stage of<br>
Apache configuration :<br><br>I get this output during the installation:<br>-------------------------------------------------------------------------------------------------------------------<br>
.<br>.<br>.<br>Apache configuration:<br> Configure Apache?: yes<br> Developer configuration: no<br> Server restart?: yes<br>Install OME servers:<br> Images (omeis): yes<br> Data (omeds): yes<br>
Web: yes<br>Apache directories:<br> httpd binary: /usr/sbin/httpd<br> apachectl binary: /usr/sbin/apachectl<br> DocumentRoot: /var/www/html<br> cgi-bin: /var/www/cgi-bin<br>
Web-UI HTML Templates: <br> Developer configuration: no<br><br>Are these values correct ? [y/n]: <br>[Fri Jan 16 09:18:40 2009] [warn] module perl_module is already loaded, skipping<br>[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.<br>
Testing Apache configuration <br> \__ mod_perl [FAILURE].<br><br><br>Errors executing task: Apache/mod_perl is not properly configured.<br>Did not get a response from <a href="http://localhost/perl2/mod_perl_test.pl" target="_blank">http://localhost/perl2/mod_perl_test.pl</a>.<br>
See /var/tmp/OME/install/ApacheConfigTask.log for more details. at (eval 187) line 1<br><br> at install.pl line 82<br> main::run_tasks() called at install.pl line 266<br># Looks like your test died before it could output anything.<br>
<br>-------------------------------------------------------------------------------------------------<br><br>The ApacheConfigTask.log show this:<br><br>Apache setup<br>Apache binary: /usr/sbin/httpd<br>apachectl binary: /usr/sbin/apachectl<br>
httpd root: /etc/httpd<br>httpd conf: /etc/httpd/conf/httpd.conf<br>httpd version: 2<br>Apache configuration:<br> Configure Apache?: yes<br> Developer configuration: no<br> Server restart?: yes<br>Install OME servers:<br>
Images (omeis): yes<br> Data (omeds): yes<br> Web: yes<br>Apache directories:<br> httpd binary: /usr/sbin/httpd<br> apachectl binary: /usr/sbin/apachectl<br>
DocumentRoot: /var/www/html<br> cgi-bin: /var/www/cgi-bin<br>Web-UI HTML Templates: <br> Developer configuration: no<br>Configuring Apache<br>httpd.conf is /etc/httpd/conf/httpd.conf<br>Installing OMEIS<br>
Copying src/C/omeis/omeis to /var/www/cgi-bin/omeis<br>chmod 0755 /var/www/cgi-bin/omeis<br>chown /var/www/cgi-bin/omeis to uid: 48 gid: 501<br>Set APACHE_OMEIS_INCLUDE to Include /OME/conf/httpd2.omeis.conf<br>Forking a process to upgrade OMEIS<br>
Installing OMEDS<br>Set APACHE_OMEDS_INCLUDE to Include /OME/conf/httpd2.omeds.conf<br>Installing WEB<br>Copying src/perl2/serve.pl to /OME/perl2/serve.pl<br>chmod 0755 /OME/perl2/serve.pl<br>chown /OME/perl2/serve.pl to uid: 48 gid: 501<br>
Copying src/html/index.html to /var/www/html/index.html<br>chmod 0644 /var/www/html/index.html<br>chmod 0644 /var/www/html/favicon.ico<br>Set APACHE_WEB_INCLUDE to Include /OME/conf/httpd2.web.conf<br>Installing DAE web by copying NonblockingSlaveWorkerCGI<br>
Copying src/perl2/OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl to /OME/perl2/NonblockingSlaveWorkerCGI.pl<br>chmod 0755 /OME/perl2/NonblockingSlaveWorkerCGI.pl<br>chown /OME/perl2/NonblockingSlaveWorkerCGI.pl to uid: 48 gid: 501<br>
Installing OME-startup.pl<br>Copying src/perl2/OME-startup.pl to /OME/conf/OME-startup.pl<br>chown /OME/conf/OME-startup.pl to uid: 48 gid: 501<br>Fixing variables in conf/httpd.ome.*.conf<br>Replacing %OME_DIST_BASE with /home/arnon/Desktop/OME-2.6.1<br>
Replacing %OME_INSTALL_BASE with /OME<br>Reading /OME/conf/httpd.ome.conf<br>Writing /OME/conf/httpd.ome.conf<br>Reading /OME/conf/httpd.omeds-dev.conf<br>Writing /OME/conf/httpd.omeds-dev.conf<br>Reading /OME/conf/httpd.omeds.conf<br>
Writing /OME/conf/httpd.omeds.conf<br>Reading /OME/conf/httpd.omeis-dev.conf<br>Writing /OME/conf/httpd.omeis-dev.conf<br>Reading /OME/conf/httpd.omeis.conf<br>Writing /OME/conf/httpd.omeis.conf<br>Reading /OME/conf/httpd.web-dev.conf<br>
Writing /OME/conf/httpd.web-dev.conf<br>Reading /OME/conf/httpd.web.conf<br>Writing /OME/conf/httpd.web.conf<br>Reading /OME/conf/httpd1.99.omeds-dev.conf<br>Writing /OME/conf/httpd1.99.omeds-dev.conf<br>Reading /OME/conf/httpd1.99.omeds.conf<br>
Writing /OME/conf/httpd1.99.omeds.conf<br>Reading /OME/conf/httpd1.99.omeis-dev.conf<br>Writing /OME/conf/httpd1.99.omeis-dev.conf<br>Reading /OME/conf/httpd1.99.omeis.conf<br>Writing /OME/conf/httpd1.99.omeis.conf<br>Reading /OME/conf/httpd1.99.web-dev.conf<br>
Writing /OME/conf/httpd1.99.web-dev.conf<br>Reading /OME/conf/httpd1.99.web.conf<br>Writing /OME/conf/httpd1.99.web.conf<br>Reading /OME/conf/httpd2.omeds-dev.conf<br>Writing /OME/conf/httpd2.omeds-dev.conf<br>Reading /OME/conf/httpd2.omeds.conf<br>
Writing /OME/conf/httpd2.omeds.conf<br>Reading /OME/conf/httpd2.omeis-dev.conf<br>Writing /OME/conf/httpd2.omeis-dev.conf<br>Reading /OME/conf/httpd2.omeis.conf<br>Writing /OME/conf/httpd2.omeis.conf<br>Reading /OME/conf/httpd2.web-dev.conf<br>
Writing /OME/conf/httpd2.web-dev.conf<br>Reading /OME/conf/httpd2.web.conf<br>Writing /OME/conf/httpd2.web.conf<br>Reading /OME/conf/httpd.ome.conf<br>Writing /OME/conf/httpd.ome.conf<br>Restarting Apache<br>Executing /usr/sbin/apachectl restart<br>
Getting an OME::Util::cURL user agent<br>Generated mod_perl test script:<br>#!/usr/bin/perl -w<br>use strict;<br>use CGI qw/-no_xhtml/;<br><br>my $CGI = CGI->new();<br>print $CGI->header(-type => 'text/plain'),<br>
<br><br>my ($key,$value);<br>while ( ($key, $value) = each %ENV)<br>{<br> print "$key = $value\n";<br>}<br><br><br>1;<br><br>Writing script to /OME/perl2/mod_perl_test.pl<br>Getting response from <a href="http://localhost/perl2/mod_perl_test.pl" target="_blank">http://localhost/perl2/mod_perl_test.pl</a><br>
Apache/mod_perl is not properly configured. Did not get a response from <a href="http://localhost/perl2/mod_perl_test.pl" target="_blank">http://localhost/perl2/mod_perl_test.pl</a>.<br><br>-----------------------------------------------------------------------------------------------------------------------------<br>
<br>When I access the file directly in my web browser "<a href="http://localhost/perl2/mod_perl_test.pl" target="_blank">http://localhost/perl2/mod_perl_test.pl</a>"<br>, this is the output I get: <br><br>SCRIPT_NAME = /perl2/mod_perl_test.pl<br>
SERVER_NAME = localhost<br>SERVER_ADMIN = root@localhost<br>HTTP_ACCEPT_ENCODING = gzip,deflate<br>HTTP_CONNECTION = keep-alive<br>REQUEST_METHOD = GET<br>HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8<br>
SCRIPT_FILENAME = /OME/perl2/mod_perl_test.pl<br>SERVER_SOFTWARE = Apache/2.2.3 (CentOS)<br>HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7<br>QUERY_STRING = <br>REMOTE_PORT = 39160<br>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<br>
SERVER_PORT = 80<br>SERVER_SIGNATURE = <address>Apache/2.2.3 (CentOS) Server at localhost Port 80</address><br><br>HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5<br>REMOTE_ADDR = 127.0.0.1<br>HTTP_KEEP_ALIVE = 300<br>
SERVER_PROTOCOL = HTTP/1.1<br>
MOD_PERL_API_VERSION = 2<br>PATH = /usr/bin/:/usr/local/bin/:/sw/bin/<br>REQUEST_URI = /perl2/mod_perl_test.pl<br>GATEWAY_INTERFACE = CGI/1.1<br>SERVER_ADDR = 127.0.0.1<br>DOCUMENT_ROOT = /var/www/html<br>HTTP_HOST = localhost<br>
MOD_PERL = mod_perl/2.0.2<br>-----------------------------------------------------------------------------------------------------------------------<br> <br>I guess it means that the script works well ...right ? so I'm not sure what is the problem...<br>
<br>Could someone please assist me in resolving this problem<br><br> <br><br>Thanks in advance, Arnon.<br><br><br><br></pre></div></div>
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</blockquote></div></div></div></div>
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