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

Tue Oct 7 16:43:05 BST 2014

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
>>>>
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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
>>
>>-------------------------------------------------------------------------
>>-------
>> ·
>
>
>

The University of Dundee is a registered Scottish Charity, No: SC015096