[ome-users] OMERO.web installation under Ubuntu 14

Wed Oct 8 14:56:35 BST 2014

Hi Simon,

Everything is working fine now!!
Thanks for your time and your patience.

Regards,
Unai

Simon Li <s.p.li at dundee.ac.uk> escribió:

> Create the directory (mkdir /home/omero/OMERO), and hopefully everything
> will work!
>
> Simon
>
> On 07/10/2014 17:30, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>
>> Hi Simon,
>>
>> sudo -i -u omero worked perfectly, thanks!
>>
>> Unluckily, the following script doesn't work:
>> $ bin/omero admin start
>> FATAL: OMERO directory does not exist: /home/omero/OMERO
>>
>> $ ls
>> examples.desktop  OMERO.server-5.0.5-ice35-b47
>> omero  OMERO.server-5.0.5-ice35-b47.zip
>> OMERO.server  settings.env
>>
>> I believe it's trying to access the OMERO repository folder once
>> again... But it's not included inside the directory.
>>
>> $ ls /home/omero
>> examples.desktop  OMERO.server-5.0.5-ice35-b47
>> omero  OMERO.server-5.0.5-ice35-b47.zip
>> OMERO.server  settings.env
>>
>>
>>
>> Unai
>>
>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>
>>> I think the problem is sudo doesn’t always setup your environment
>>> correctly (e.g. The $HOME variable isn’t always updated), could you try
>>> either:
>>> sudo -i -u omero
>>> Or if that fails:
>>> su - omero
>>>
>>> Simon
>>>
>>> On 07/10/2014 14:38, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es> wrote:
>>>
>>>> Hi Simon
>>>>
>>>> I haven't set any enviroment variable.
>>>>
>>>> I login as the omero user using:
>>>> $sudo -s -u omero
>>>>
>>>> Regards,
>>>> Unai
>>>>
>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>
>>>>> Hi Unai
>>>>>
>>>>> It looks like OMERO is trying to write to a non-standard temporary
>>>>> directory. Have you set any environment variables? Try running
>>>>>
>>>>> $ set | grep -E 'TEMP|TMP'
>>>>>
>>>>> How did you logon as the omero user- with sudo, su, or directly?
>>>>>
>>>>> Simon
>>>>>
>>>>> P.S. When you reply could you ensure you use reply-all so that
>>>>> ome-users at lists.openmicroscopy.org.uk gets copied in.
>>>>>
>>>>> On 07/10/2014 11:40, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>> wrote:
>>>>>
>>>>>> Hi Simon,
>>>>>>
>>>>>> Thanks for the tip yo gave me yesterday! I set the correct path and I
>>>>>> could finally download and unzip OMERO.web.
>>>>>>
>>>>>> Unluckily, I get more permission errors while I'm setting
>>>>>> OMERO.server
>>>>>> as the omero system user. At some point, the script is trying to
>>>>>> acces
>>>>>> the administrator account:
>>>>>>
>>>>>> omero at imServer:/home/omero$ OMERO.server/bin/omero config set
>>>>>> omero.db.name "$OMERO_DB_NAME"
>>>>>> + OMERO.server/bin/omero config set omero.db.name omeroubf
>>>>>> WARNING:omero.util.TempFileManager:Invalid tmp dir: /home/jribecarios
>>>>>> Traceback (most recent call last):
>>>>>>   File
>>>>>> "/home/omero/OMERO.server/lib/python/omero/util/temp_files.py", line
>>>>>> 166, in tmpdir
>>>>>>     name = self.mkstemp(prefix=".lock_test", suffix=".tmp",
>>>>>> dir=target)
>>>>>>   File
>>>>>> "/home/omero/OMERO.server/lib/python/omero/util/temp_files.py", line
>>>>>> 246, in mkstemp
>>>>>>     fd, name = tempfile.mkstemp(prefix = prefix, suffix = suffix, dir
>>>>>> = dir, text = text)
>>>>>>   File "/usr/lib/python2.7/tempfile.py", line 308, in mkstemp
>>>>>>     return _mkstemp_inner(dir, prefix, suffix, flags)
>>>>>>   File "/usr/lib/python2.7/tempfile.py", line 239, in _mkstemp_inner
>>>>>>     fd = _os.open(file, flags, 0600)
>>>>>> OSError: [Errno 13] Permission denied:
>>>>>> '/home/jribecarios/.lock_testrsfzij.tmp'
>>>>>>
>>>>>> I don't really understand why, because apparently the omero user
>>>>>> account has been set as the owner of the /OMERO folder, inside the
>>>>>> administrator account.
>>>>>> Does it mean that the OMERO repository should be also set inside the
>>>>>> omero user account?
>>>>>>
>>>>>> Cheers,
>>>>>> Unai
>>>>>>
>>>>>>
>>>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>>>
>>>>>>> Hi Unai
>>>>>>>
>>>>>>> Which directory were you in (run `pwd` if you’re not sure) when you
>>>>>>> ran
>>>>>>> wget?
>>>>>>>
>>>>>>> Simon
>>>>>>>
>>>>>>> On 06/10/2014 15:19, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>>>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Dear Simon,
>>>>>>>>
>>>>>>>> Since I had so much problems trying to install OMERO I decided to
>>>>>>>> reset the computer, rei-nstall Ubuntu 14.04, and try to install
>>>>>>>> OMERO
>>>>>>>> once again from the beginning, following these instructions:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/ser
>>>>>>>> ve
>>>>>>>> r-
>>>>>>>> li
>>>>>>>> nux-walkthrough.html
>>>>>>>>
>>>>>>>> According to them, I created an omero system user:
>>>>>>>> useradd -m omero
>>>>>>>> chmod a+X ~omero
>>>>>>>>
>>>>>>>> Then I got "permission denied" errors when I tried to download and
>>>>>>>> unzip OMERO.server as the omero system user with the following
>>>>>>>> code:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> SERVER=http://downloads.openmicroscopy.org/omero/5.0.5/artifacts/OME
>>>>>>>> RO
>>>>>>>> .s
>>>>>>>> er
>>>>>>>> ver-5.0.5-ice35-b47.zip
>>>>>>>> wget $SERVER
>>>>>>>> unzip -q `basename $SERVER`
>>>>>>>>
>>>>>>>> If I use "sudo" with both commands, the terminal needs the password
>>>>>>>> of
>>>>>>>> the omero account to execute them, and it hasn't been set (for
>>>>>>>> safety
>>>>>>>> reason, I guess...).
>>>>>>>>
>>>>>>>> Should I create the omero system user with more permissions? Do you
>>>>>>>> think is a good idea to create an omero system user with a password
>>>>>>>> and sudo wget and unzip?
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Unai
>>>>>>>>
>>>>>>>>
>>>>>>>> Simon Li <s.p.li at dundee.ac.uk> escribió:
>>>>>>>>
>>>>>>>>> On 02/10/2014 12:36, "unai_lorenzo at ehu.es" <unai_lorenzo at ehu.es>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Dear Simon,
>>>>>>>>>>
>>>>>>>>>> I symlinked the 'nginx.conf.template' file to the
>>>>>>>>>> '/etc/nginx/sites-enabled' folder, restarted nginx, and I
>>>>>>>>>> couldn't
>>>>>>>>>> success once again.
>>>>>>>>>
>>>>>>>>> Did you check both port 80 and 8080? You might need to disable
>>>>>>>>> sites-available/default.
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Appart from that I've also tried to login from OMERO.insight,
>>>>>>>>>> and I
>>>>>>>>>> couldn't run the 'OMEROinsight_unix.sh' file from the terminal
>>>>>>>>>> due
>>>>>>>>>> to
>>>>>>>>>> an abnormal termination:
>>>>>>>>>>
>>>>>>>>>> Abnormal termination due to an uncaught exception.
>>>>>>>>>> java.awt.HeadlessException
>>>>>>>>>
>>>>>>>>> This is a separate issue. It could be because the server
>>>>>>>>> walkthrough
>>>>>>>>> assumes you¹ll be running Insight from a different computer, so
>>>>>>>>> the
>>>>>>>>> headless version of Java is specified (openjdk-7-jre-headless) to
>>>>>>>>> reduce
>>>>>>>>> the number of dependencies that are instacommandlled.
>>>>>>>>>
>>>>>>>>> You could try installing the full JRE instead:
>>>>>>>>> apt-get install openjdk-7-jre
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Simon
>>>>>>>>> command
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.jav
>>>>>>>>>> a:
>>>>>>>>>> 20
>>>>>>>>>> 7)
>>>>>>>>>> at java.awt.Window.<init>(Window.java:535)
>>>>>>>>>> at java.awt.Frame.<init>(Frame.java:420)
>>>>>>>>>> at javax.swing.JFrame.<init>(JFrame.java:218)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenL
>>>>>>>>>> og
>>>>>>>>>> in
>>>>>>>>>> .j
>>>>>>>>>> av
>>>>>>>>>> a:1033)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedVi
>>>>>>>>>> ew
>>>>>>>>>> (S
>>>>>>>>>> pl
>>>>>>>>>> as
>>>>>>>>>> hScreenManager.java:176)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(Splash
>>>>>>>>>> Sc
>>>>>>>>>> re
>>>>>>>>>> en
>>>>>>>>>> Ma
>>>>>>>>>> nager.java:241)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashSc
>>>>>>>>>> re
>>>>>>>>>> en
>>>>>>>>>> Pr
>>>>>>>>>> ox
>>>>>>>>>> y.java:123)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFact
>>>>>>>>>> or
>>>>>>>>>> y.
>>>>>>>>>> ja
>>>>>>>>>> va
>>>>>>>>>> :59)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(Splash
>>>>>>>>>> Sc
>>>>>>>>>> re
>>>>>>>>>> en
>>>>>>>>>> In
>>>>>>>>>> it.java:99)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.
>>>>>>>>>> ja
>>>>>>>>>> va
>>>>>>>>>> :2
>>>>>>>>>> 76
>>>>>>>>>> )
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.Container.runStartupProcedure(Contai
>>>>>>>>>> ne
>>>>>>>>>> r.
>>>>>>>>>> ja
>>>>>>>>>> va
>>>>>>>>>> :128)
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> org.openmicroscopy.shoola.env.Container.access$000(Container.java:
>>>>>>>>>> 78
>>>>>>>>>> )
>>>>>>>>>> at
>>>>>>>>>> org.openmicroscopy.shoola.env.Container$1.run(Container.java:174)
>>>>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>>>>>>> Exception in thread "Initializer"
>>>>>>>>>>
>>>>>>>>>> Exception: java.awt.HeadlessException thrown from the
>>>>>>>>>> UncaughtExceptionHandler in thread "Initializer"
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Maybe this error is related to the connection problems, or maybe
>>>>>>>>>> this
>>>>>>>>>> is an extra problem...
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Unai
>>>>>>>>>> command
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>>>>> SC015096
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ---------------------------------------------------------------------
>>>>>>> --
>>>>>>> --
>>>>>>> -------
>>>>>>> ·
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>> --
>>>>> -------
>>>>> ·
>>>>
>>>>
>>>>
>>>
>>>
>>> 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
>>>
>>> -------------------------------------------------------------------------
>>> -------
>>> ·
>>
>>
>>
>
>
> 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
> --------------------------------------------------------------------------------
> ·