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

Tue Oct 7 17:30:07 BST 2014

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/serve
>>>>>> 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/OMERO
>>>>>> .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.java:
>>>>>>>> 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>(ScreenLog
>>>>>>>> in
>>>>>>>> .j
>>>>>>>> av
>>>>>>>> a:1033)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView
>>>>>>>> (S
>>>>>>>> pl
>>>>>>>> as
>>>>>>>> hScreenManager.java:176)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashSc
>>>>>>>> re
>>>>>>>> en
>>>>>>>> Ma
>>>>>>>> nager.java:241)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScre
>>>>>>>> en
>>>>>>>> Pr
>>>>>>>> ox
>>>>>>>> y.java:123)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactor
>>>>>>>> y.
>>>>>>>> ja
>>>>>>>> va
>>>>>>>> :59)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashSc
>>>>>>>> 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(Containe
>>>>>>>> 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
> --------------------------------------------------------------------------------
> ·