Open Microscopy Environment

I'm now installing the nginx web server. when I try and run

su - omero -c "bash -eux setup_omero.ginx.sh"

I receive the error

bash: setup_omero.nginx.sh: No such file or directory

do I need to point to setup_omero.nginx.sh? If so where is the file located or how do I fix this problem?

Shane

Dear Shane

Sorry for the confusion
it seems that the file is not available in our documentation (that's a bug)
We will fix that in the next coming release.
It has not been correctly copied from the following repo https://github.com/ome/omero-install

Here is a link to the file you are looking for
https://github.com/ome/omero-install/bl ... o_nginx.sh

Alternatively you could run the following commands, as the omero user:

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OMERO.server/bin/omero config set omero.web.application_server wsgi-tcp
OMERO.server/bin/omero web config nginx --http "$OMERO_WEB_PORT" > OMERO.server/nginx.conf.tmp

where $OMERO_WEB_PORT is your chosen port e.g. 80


Regards

Jmarie

it seems that the file is not available in our documentation (that's a bug)

Ah that explains it. I ran the rest of the code you gave me and everything came back fine...

when I try and run OMERO i run into problems in the first steps...

The following steps are run as the omero system user.

OMERO should now be set up. To start the server run:

OMERO.server/bin/omero admin start
If you deploy with Nginx, to start the OMERO.web client run:

OMERO.server/bin/omero web start

when I try and run these lines it gives me an OMERO.server/bin/omero No such file or directory error.

When i manually go into /OMERO.server/bin/ and type omero admin start

I get -su: omero: command not found...

any ideas? The omero that I see when i use the "ls" command is green, which I looked it up its says thats a datafile... did I do something wrong?

Hi Shane,

If you're actually in the /bin directory, you can run the omero command with ./omero.
E.g.

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$ cd bin
$ ./omero config get


Hope that helps,

Will.

huh. When I use ./omero config get It returns my omero.data.dir and omero.db.name inputs (All of them I believe) but ./omero admin start says

FATAL: OMERO directory does not exist: OMERO

although when I run ./omero web start the OMERO.web starts I believe. As I go the message

Starting OMERO.web... [OK]

any ideas on ./omero admin start?

shaneklumpp wrote:huh. When I use ./omero config get It returns my omero.data.dir and omero.db.name inputs (All of them I believe) but ./omero admin start says

FATAL: OMERO directory does not exist: OMERO

although when I run ./omero web start the OMERO.web starts I believe. As I go the message

Starting OMERO.web... [OK]

any ideas on ./omero admin start?

That looks like you missed the step to create binary repository

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mkdir -p "$OMERO_DATA_DIR"
chown omero "$OMERO_DATA_DIR"

and then make sure the same directory is set in

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OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"

once is set try to start the server

Ola

Thank you so much. I had asked earlier where I was supposed to put the binary OMERO directory but received no clarification. Thanks for helping me find the right place for it!

./omero admin start and ./omero web start now are working!

Just a clarification question here, I'm working on the section to get OMERO and OMERO.web to run automatically when the server starts up and had some questions about omero-init.d and omero-web-init.d

for example in this code:

OMERO_SERVER=${OMERO_SERVER:-/home/omero/OMERO.server}
OMERO_USER=${OMERO_USER:-omero}
OMERO=${OMERO_SERVER}/bin/omero

start() {
echo -n $"Starting $prog:"
su - ${OMERO_USER} -c "${OMERO} admin start" &> /dev/null && echo -n ' OMERO.server'
RETVAL=$?
[ "$RETVAL" = 0 ]
echo
}

There are several environmental variables (I believe) such as ${OMERO_USER}, am I supposed to replace that with my OMERO_USER which is just omero? or should I leave the file perfectly as is and just use it as a copy-paste method?

Thanks,

Shane

Hi Shane,

shaneklumpp wrote:

OMERO_SERVER=${OMERO_SERVER:-/home/omero/OMERO.server}
...
There are several environmental variables (I believe) such as ${OMERO_USER}, am I supposed to replace that with my OMERO_USER which is just omero? or should I leave the file perfectly as is and just use it as a copy-paste method?

The syntax "X=${X:-foo}" means "If X is set use X, otherwise use the default of 'foo'". So the script should default to setting "OMERO_USER" to "omero" unless you set it to something else.

Cheers,
~Josh

Perfect I'll leave it as is then as my OMERO_USER is just omero.

Thanks Josh,
Shane

having a problem when I try to run ./omero admin start

is there a way to check if omero admin start worked and that omero is running?

when i run ./omero admin start I get

omero@ip-172-31-18-162:~/OMERO.server/bin$ ./omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit

and then the command line pops up again. Does that mean it is running? How can I test this?