[ome-users] OMERO.web installation under Ubuntu 14
Simon Li
s.p.li at dundee.ac.uk
Wed Oct 1 20:35:20 BST 2014
Hi Unai
/etc/nginx is a system directory on the server's root partition, it's
not part of OMERO.server.
Simon
On Wed, 2014-10-01 at 18:11 +0200, unai_lorenzo at ehu.es wrote:
> 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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> >>>>>>
> >>>>>
> >>>>>
> >>>>> The University of Dundee is a registered Scottish Charity, No:
> >>>>> SC015096
> >>>>>
> >>>>> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de
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> >>>>> -----------------------------------------------------------------------
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> >>>>> ·
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> The University of Dundee is a registered Scottish Charity, No: SC015096
> >>>
> >>> Esta cabecera ha sido añadida automáticamente por la Vicegerencia de
> >>> las TIC:
> >>>
> >>> -------------------------------------------------------------------------
> >>> -------
> >>> 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)
> >>> UPV/EHU, IKT Gerenteordetza
> >>>
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> >>> -------
> >>> ·
> >>
> >>
> >>
> >> _______________________________________________
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> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> > Esta cabecera ha sido añadida automáticamente por la Vicegerencia de las TIC:
> > --------------------------------------------------------------------------------
> > 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)
> > UPV/EHU, IKT Gerenteordetza
> > --------------------------------------------------------------------------------
> > ·
>
>
>
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