[ome-users] OMERO.web installation under Ubuntu 14
unai_lorenzo at ehu.es
unai_lorenzo at ehu.es
Wed Oct 1 17:11:31 BST 2014
Hi Simon,
Maybe that's the problem...
While I was following the installation protocol I skipped that step
because I didn't find any folder called '/nginx'. The only folders
included in the '/etc' directory are '/etc/grid' and '/etc/profiles'.
Could you please tell me when and how this folder is generated ?
Cheers,
Unai
Simon Li <s.p.li at dundee.ac.uk> escribió:
> Can I just check you copied or symlinked the config to
> /etc/nginx/sites-enabled, and restarted nginx?
>
> Simon
>
> On 01/10/2014 11:52, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>
>> Hi Simon,
>> I'm using Ubuntu 14.04 LTS.
>>
>> I've been following OMERO.server installation
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-i
>> nstallation.html), OMERO.server Linux walkthrough
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-l
>> inux-walkthrough.html), and OMERO.web deployment
>> (http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/install-
>> web.html).
>>
>> I generated the nginx configuration with 'bin/omero web config nginx
>> --system'.
>> The first lines that the command returned are:
>> listen 8080;
>> server_name $hostname;
>>
>>
>> I installed nginx at the same time as Ice, Java and Postgres. I used
>> the following command (as suggested in the walkthrough):
>>
>> apt-get -y install \
>> unzip \
>> wget \
>> python-{imaging,matplotlib,numpy,pip,scipy,tables,virtualenv} \
>> openjdk-7-jre-headless \,
>> ice-services python-zeroc-ice \
>> postgresql \
>> nginx
>>
>> Thanks for your help,
>> Unai
>>
>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>
>>> Hi Unai
>>>
>>> What operating system and version are you using? Which set of
>>> instructions
>>> were you following- the ones from
>>>
>>> https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/install
>>> -w
>>> eb.html or the walkthrough at
>>>
>>> https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-
>>> li
>>> nux-walkthrough.html ?
>>>
>>> Did you generate your nginx config with 'bin/omero web config nginx
>>> --system’? And finally, how did you install this nginx config?
>>>
>>> Thanks
>>>
>>> Simon
>>>
>>> On 30/09/2014 16:25, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>>>
>>>> Hi Simon,
>>>>
>>>> Unluckily your suggestions didn't work either.
>>>>
>>>> When I try to access OMERO.web on port 80 I can see the following
>>>> message:
>>>> Welcome to nginx!
>>>> If you see this page, the nginx web server is successfully installed
>>>> and working. Further configuration is required.
>>>>
>>>> And if I try to access OMERO.web on port 8080 the address is not
>>>> valid. Does it mean that I should configure Apache or Nginx to listen
>>>> to 8080 port?
>>>>
>>>> Thanks again!!
>>>> Unai
>>>>
>>>>
>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>
>>>>> Hi Unai
>>>>>
>>>>> Could you try unsetting all of your omero.web.* configuration options,
>>>>> regenerate your nginx or apache configuration files, restart OMERO and
>>>>> OMERO.web, and seeing if that works?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Simon
>>>>>
>>>>> On 30/09/2014 08:34, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>> wrote:
>>>>>
>>>>>> Dear Simon,
>>>>>>
>>>>>> I'm using nginx/apache.
>>>>>> I've also tried to access OMERO.web on the ports you suggested but it
>>>>>> didn't work either.
>>>>>> This is the output of `bin/omero config get':
>>>>>>
>>>>>> omero.data.dir=/home/jribecarios/OMERO
>>>>>> omero.db.name=omero_database
>>>>>> omero.db.pass=db_password
>>>>>> omero.db.user=db_user
>>>>>> omero.web.application_server=fastcgi
>>>>>> omero.web.application_server.host=localhost
>>>>>> omero.web.application_server.port=4080
>>>>>> omero.web.force_script_name=/omero
>>>>>> omero.web.static_url=/omero/static/
>>>>>> jribecarios at jribecarios:~/omero/OMERO.server-5.0.4-ice35-b43$
>>>>>>
>>>>>>
>>>>>> I hope it helps.
>>>>>>
>>>>>> Many thanks,
>>>>>> Unai
>>>>>>
>>>>>>
>>>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>>>
>>>>>>> Hi Unai
>>>>>>>
>>>>>>> Are you using the development web server, or nginx/apache? If it¹s
>>>>>>> the
>>>>>>> latter then OMERO.web should be accessible on either port 80 or 8080
>>>>>>> depending on your configuration, port 4080 is used for internal
>>>>>>> communication.
>>>>>>>
>>>>>>> If this doesn¹t solve your problem could you paste the output of
>>>>>>> `bin/omero config get`?
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Simon
>>>>>>>
>>>>>>> On 29/09/2014 16:58, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear OME users,
>>>>>>>>
>>>>>>>> I am trying to install OMERO.web under Ubuntu 14. I've been
>>>>>>>> following
>>>>>>>> all the instructions included in the web page, and everything seems
>>>>>>>> to
>>>>>>>> be OK: I could start the server, and the OMERO.web client.
>>>>>>>>
>>>>>>>> $ bin/omero web start
>>>>>>>>
>>>>>>>> 0 static files copied, 816 unmodified.
>>>>>>>> Starting OMERO.web... [OK]
>>>>>>>>
>>>>>>>>
>>>>>>>> But I can't access OMERO.webadmin on the following address
>>>>>>>> http://localhost:4080.
>>>>>>>>
>>>>>>>> Any guess about what's wrong? Could it be the something related to
>>>>>>>> the
>>>>>>>> the firewall and the TCP ports?
>>>>>>>>
>>>>>>>>
>>>>>>>> Here you will find the diagnostics:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ====================================================================
>>>>>>>> ==
>>>>>>>> ==
>>>>>>>> ==
>>>>>>>> ======
>>>>>>>> OMERO Diagnostics 5.0.4-ice35-b43
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ====================================================================
>>>>>>>> ==
>>>>>>>> ==
>>>>>>>> ==
>>>>>>>> ======
>>>>>>>>
>>>>>>>> WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:Please upgrade to
>>>>>>>> 5.0.5 See http://trac.openmicroscopy.org.uk/omero for the latest
>>>>>>>> version
>>>>>>>>
>>>>>>>> Commands: java -version 1.7.0
>>>>>>>> (/usr/bin/java)
>>>>>>>> Commands: python -V 2.7.6
>>>>>>>> (/usr/bin/python)
>>>>>>>> Commands: icegridnode --version 3.5.1
>>>>>>>> (/usr/bin/icegridnode)
>>>>>>>> Commands: icegridadmin --version 3.5.1
>>>>>>>> (/usr/bin/icegridadmin)
>>>>>>>> Commands: psql --version 9.3.5
>>>>>>>> (/usr/bin/psql)
>>>>>>>>
>>>>>>>> Server: icegridnode running
>>>>>>>> Server: Blitz-0 active (pid = 4371,
>>>>>>>> enabled)
>>>>>>>> Server: DropBox active (pid = 4403,
>>>>>>>> enabled)
>>>>>>>> Server: FileServer active (pid = 4404,
>>>>>>>> enabled)
>>>>>>>> Server: Indexer-0 active (pid = 4383,
>>>>>>>> enabled)
>>>>>>>> Server: MonitorServer active (pid = 4387,
>>>>>>>> enabled)
>>>>>>>> Server: OMERO.Glacier2 active (pid = 4394,
>>>>>>>> enabled)
>>>>>>>> Server: OMERO.IceStorm active (pid = 4420,
>>>>>>>> enabled)
>>>>>>>> Server: PixelData-0 active (pid = 4410,
>>>>>>>> enabled)
>>>>>>>> Server: Processor-0 active (pid = 4416,
>>>>>>>> enabled)
>>>>>>>> Server: Tables-0 active (pid = 4412,
>>>>>>>> enabled)
>>>>>>>> Server: TestDropBox inactive (enabled)
>>>>>>>>
>>>>>>>> OMERO: SSL port 4064
>>>>>>>> OMERO: TCP port 4063
>>>>>>>>
>>>>>>>> Log dir:
>>>>>>>> /home/jribecarios/omero/OMERO.server-5.0.4-ice35-b43/var/log exists
>>>>>>>>
>>>>>>>> Log files: Blitz-0.log 672.0 KB errors=12
>>>>>>>> warnings=6
>>>>>>>> Log files: DropBox.log 3.0 KB errors=0
>>>>>>>> warnings=1
>>>>>>>> Log files: FileServer.log 0.0 KB
>>>>>>>> Log files: Indexer-0.log 21.0 KB errors=13
>>>>>>>> warnings=0
>>>>>>>> Log files: MonitorServer.log 2.0 KB
>>>>>>>> Log files: OMEROweb.log 0.0 KB
>>>>>>>> Log files: OMEROweb_request.log 0.0 KB
>>>>>>>> Log files: PixelData-0.log 25.0 KB errors=18
>>>>>>>> warnings=1
>>>>>>>> Log files: Processor-0.log 2.0 KB errors=0
>>>>>>>> warnings=1
>>>>>>>> Log files: Tables-0.log 2.0 KB
>>>>>>>> Log files: TestDropBox.log n/a
>>>>>>>> Log files: master.err 2.0 KB errors=0
>>>>>>>> warnings=4
>>>>>>>> Log files: master.out 0.0 KB
>>>>>>>> Log files: Total size 0.73 MB
>>>>>>>>
>>>>>>>>
>>>>>>>> Environment:OMERO_HOME=(unset)
>>>>>>>> Environment:OMERO_NODE=(unset)
>>>>>>>> Environment:OMERO_MASTER=(unset)
>>>>>>>> Environment:OMERO_TEMPDIR=(unset)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/
>>>>>>>> sb
>>>>>>>> in
>>>>>>>> :/
>>>>>>>> bin:/usr/games:/usr/local/games
>>>>>>>> Environment:PYTHONPATH=(unset)
>>>>>>>> Environment:ICE_HOME=(unset)
>>>>>>>> Environment:LD_LIBRARY_PATH=(unset)
>>>>>>>> Environment:DYLD_LIBRARY_PATH=(unset)
>>>>>>>>
>>>>>>>> OMERO data dir: '/home/jribecarios/OMERO'Exists? TrueIs writable?
>>>>>>>> True
>>>>>>>> OMERO temp dir: '/home/jribecarios/omero/tmp'Exists? TrueIs
>>>>>>>> writable? True (Size: 0)
>>>>>>>> OMERO.web status... [RUNNING] (PID 11366)
>>>>>>>>
>>>>>>>>
>>>>>>>> Many thanks in advance!!
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Unai
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> ome-users mailing list
>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>
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>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de las TIC:
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> ATENCION!! Este correo contiene la palabra "contraseña" y puede
> tratarse de un fraude.
> No proporcione nunca sus credenciales por correo electrónico.
> Si tiene alguna duda consulte con el CAU (154400).
> UPV/EHU, Vicegerencia de las TIC
>
> ERNE!! Mezu honek "contraseña" hitza dauka eta iruzurrezko mezua
> izan daiteke.
> Ez eman inoiz zure pasahitza posta elektronikoaren bidez.
> Zalantzarik izanez gero deitu BAZren telefonora (154400)
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