Open Microscopy Environment

Hi,

Based on the URl http://docs.openmicroscopy.org/omero/5. ... ice36.html
we tried the installation.during this we have some question on installation steps

1.Kindly mention the login credential in the top the Installation Commons (like need to root or the omero user)
Because we installed in root and some of the steps show error like

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[root@localhost omero]# OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
FATAL: Running OMERO.server/bin/omero as root can corrupt your directory permissions.
[root@localhost omero]# su omero
[omero@localhost ~]$ OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
[Errno 13] Permission denied: '/home/omero/OMERO.server/etc/grid/config.xml'


And during creation of User and directory for the OMERO repository installation we received this message

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[root@localhost ~]# mkdir -p "$OMERO_DATA_DIR"
mkdir: cannot create directory ‘’: No such file or directory
[root@localhost ~]# pwd
/root
[root@localhost ~]#
[root@localhost omero]# mkdir -p "$OMERO_DATA_DIR"
mkdir: cannot create directory ‘’: No such file or directory
[root@localhost omero]# pwd
/home/omero
[root@localhost omero]#

Kindly mention where to create this folder ? in which login root or omero ?

And in http://docs.openmicroscopy.org/omero/5. ... ce3.6.html

Configure OMERO.web and generate nginx template (run as omero): During this we recevied this error

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[omero@localhost ~]$ /home/omero/OMERO.py/bin/omero web config nginx --http "80" --servername "localhost" > /home/omero/nginx.conf.tmp
ERROR: Django not installed!


Hi,

Did you run these commands as the 'omero' user?

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SERVER=http://downloads.openmicroscopy.org/latest/omero5.3/server-ice36.zip
wget $SERVER -O OMERO.server-ice36.zip
unzip -q OMERO.server*


The error "Permission denied: '/home/omero/OMERO.server/etc/grid/config.xml'" suggests that the OMERO.server belongs to the root user?

mkdir -p "$OMERO_DATA_DIR"
probably failed because in switching between root and omero users, the OMERO_DATA_DIR variable got lost.

You can repeat the export:

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# to see whether this variable is still available
echo $OMERO_DATA_DIR

# to reset it in current user context
export OMERO_DATA_DIR=/OMERO

mkdir -p "$OMERO_DATA_DIR"


You should run this as root, but then change the owner to omero as described.


Django should have been installed in this line:

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/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt


Hope that helps,

Will.

Hi,

Thanks for sorting the two issues.

Still i have issue in Configure OMERO.web and generate nginx template (run as omero):

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[omero@localhost ~]$ /home/omero/OMERO.py/bin/omero web config nginx --http "${80}" --servername "${localhost}" > /home/omero/nginx.conf.tmp
usage: /home/omero/OMERO.py/bin/omero web config [-h] [--http HTTP]
                                                 [--servername SERVERNAME]
                                                 [--max-body-size MAX_BODY_SIZE]

                                                 {nginx,nginx-development,apache22,apache24,apache}
/home/omero/OMERO.py/bin/omero web config: error: argument --http: invalid int value: ''


if issue with setting the environment value mean where to i set those ?

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OMERO_USER=omero
WEBPORT=80
WEBSERVER_NAME=localhost

I am struck in this step Configure OMERO.web and generate nginx template (run as omero)

Hi mayav,

You have used:

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--http "${80}"

This would be using the content of a variable named $80, which doesn't exist.

The top of http://docs.openmicroscopy.org/omero/5. ... ce3.6.html states
"When following this walkthrough you can either use your own values, or alternatively source the following file:"

So it's as you'll have done in the other walkthrough, either use "source" to have the variables "OMERO_USER", "WEBPORT" and "WEBSERVER NAME" set, or change any use of a variable in the walkthrough, e.g.

from

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omero web config nginx --http "${WEBPORT}"

to

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omero web config nginx --http 80

Best,

Kenny

Hi,

Thanks for fast reply
Its working.

I have one more question i got this error message

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systemctl start omero-web.service
Job for omero-web.service failed because the control process exited with error code. See "systemctl status omero-web.service" and "journalctl -xe" for details.


Here with i attached the output of journalctl -xe

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Sep 18 16:47:48 localhost.localdomain sshd[5704]: pam_unix(sshd:session): session opened for user root by (uid=0)
Sep 18 16:48:42 localhost.localdomain polkitd[936]: Registered Authentication Agent for unix-process:5716:85635 (system bus name :1.24 [/usr/bin/pkttyagent --notify-fd 5 --fallback], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Sep 18 16:48:42 localhost.localdomain systemd[1]: Reloading.
Sep 18 16:48:42 localhost.localdomain systemd[1]: Configuration file /usr/lib/systemd/system/ebtables.service is marked executable. Please remove executable permission bits. Proceeding anyway.
Sep 18 16:48:43 localhost.localdomain polkitd[936]: Unregistered Authentication Agent for unix-process:5716:85635 (system bus name :1.24, object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8) (disconnected from bus)
Sep 18 16:48:46 localhost.localdomain polkitd[936]: Registered Authentication Agent for unix-process:5735:86012 (system bus name :1.25 [/usr/bin/pkttyagent --notify-fd 5 --fallback], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Sep 18 16:48:46 localhost.localdomain systemd[1]: Reloading.
Sep 18 16:48:46 localhost.localdomain systemd[1]: Configuration file /usr/lib/systemd/system/ebtables.service is marked executable. Please remove executable permission bits. Proceeding anyway.
Sep 18 16:48:46 localhost.localdomain polkitd[936]: Unregistered Authentication Agent for unix-process:5735:86012 (system bus name :1.25, object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8) (disconnected from bus)
Sep 18 16:48:51 localhost.localdomain polkitd[936]: Registered Authentication Agent for unix-process:5753:86484 (system bus name :1.26 [/usr/bin/pkttyagent --notify-fd 5 --fallback], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Sep 18 16:48:51 localhost.localdomain systemd[1]: Starting OMERO.web...
-- Subject: Unit omero-web.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit omero-web.service has begun starting up.
Sep 18 16:48:51 localhost.localdomain systemd[5759]: Failed at step EXEC spawning /home/omero/omerowebvenv/venv/python: No such file or directory
-- Subject: Process /home/omero/omerowebvenv/venv/python could not be executed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- The process /home/omero/omerowebvenv/venv/python could not be executed and failed.
--
-- The error number returned by this process is 2.
Sep 18 16:48:51 localhost.localdomain systemd[1]: omero-web.service: control process exited, code=exited status=203
Sep 18 16:48:51 localhost.localdomain systemd[1]: Failed to start OMERO.web.
-- Subject: Unit omero-web.service has failed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit omero-web.service has failed.
--
-- The result is failed.
Sep 18 16:48:51 localhost.localdomain systemd[1]: Unit omero-web.service entered failed state.
Sep 18 16:48:51 localhost.localdomain systemd[1]: omero-web.service failed.
Sep 18 16:48:51 localhost.localdomain polkitd[936]: Unregistered Authentication Agent for unix-process:5753:86484 (system bus name :1.26, object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8) (disconnected from bus)
Sep 18 16:48:58 localhost.localdomain polkitd[936]: Registered Authentication Agent for unix-process:5762:87231 (system bus name :1.27 [/usr/bin/pkttyagent --notify-fd 5 --fallback], object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8)
Sep 18 16:48:58 localhost.localdomain systemd[1]: Starting OMERO.web...
-- Subject: Unit omero-web.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit omero-web.service has begun starting up.
Sep 18 16:48:58 localhost.localdomain systemd[5768]: Failed at step EXEC spawning /home/omero/omerowebvenv/venv/python: No such file or directory
-- Subject: Process /home/omero/omerowebvenv/venv/python could not be executed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- The process /home/omero/omerowebvenv/venv/python could not be executed and failed.
--
-- The error number returned by this process is 2.
Sep 18 16:48:58 localhost.localdomain systemd[1]: omero-web.service: control process exited, code=exited status=203
Sep 18 16:48:58 localhost.localdomain systemd[1]: Failed to start OMERO.web.
-- Subject: Unit omero-web.service has failed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit omero-web.service has failed.
--
-- The result is failed.
Sep 18 16:48:58 localhost.localdomain systemd[1]: Unit omero-web.service entered failed state.
Sep 18 16:48:58 localhost.localdomain systemd[1]: omero-web.service failed.
Sep 18 16:48:58 localhost.localdomain polkitd[936]: Unregistered Authentication Agent for unix-process:5762:87231 (system bus name :1.27, object path /org/freedesktop/PolicyKit1/AuthenticationAgent, locale en_US.UTF-8) (disconnected from bus)
Sep 18 16:49:59 localhost.localdomain systemd[1]: Starting Cleanup of Temporary Directories...
-- Subject: Unit systemd-tmpfiles-clean.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit systemd-tmpfiles-clean.service has begun starting up.
Sep 18 16:49:59 localhost.localdomain systemd[1]: Started Cleanup of Temporary Directories.
-- Subject: Unit systemd-tmpfiles-clean.service has finished start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit systemd-tmpfiles-clean.service has finished starting up.
--
-- The start-up result is done.


mayav wrote:Here with i attached the output of journalctl -xe

Your error output contained:
"/home/omero/omerowebvenv/venv/python: No such file or directory"

Did you follow the "optional" virtualenv steps in the walkthrough?

* Install VirtualEnv - optional (run as root):
* Install in the virtualenv created previously (run as root):

If you didn't run these, then you'll need to update your `omero-web-systemd.service` file such that it doesn't reference the non-existent Python virtualenv.

Hi,

We installed the "optional" virtualenv steps
still it showing same error message


in the file we have

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Environment="PATH=/home/omero/omerowebvenv/venv/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
ExecStart=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web start
ExecStop=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web stop

but no directory called venv in the location ?

Hi mayav,

Aha, I see the problem. We've got a fix for this ready for the next version of our documentation.

cf https://github.com/ome/omeroweb-install/pull/20/files

Just remove `venv/` from the paths, so they read: e.g.

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Environment="PATH=/home/omero/omerowebvenv/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
ExecStart=/home/omero/omerowebvenv/python $WEBBINDIR/omero web start
ExecStop=/home/omero/omerowebvenv/python $WEBBINDIR/omero web stop


All the best,

Kenny

Hello
The documentation is not correct
A similar problem was reported in the following post viewtopic.php?f=5&t=8346.
We have fixed the instruction https://github.com/ome/omeroweb-install/pull/20 and improve the walkthrough.
The changes will be part of the coming 5.4.0 release

Cheers
Jmarie

Thanks for the update,

When will we receive the next Release version and Document ?