[ome-users] OMERO.web installation under Ubuntu 14
Simon Li
s.p.li at dundee.ac.uk
Tue Oct 7 18:14:59 BST 2014
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
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