Open Microscopy Environment

Dear all

I've been happily working my way through a new installation and I've got to the point where I'm trying to read in the initial database. So I ran the following without any problems...

OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
OMERO.server/bin/omero config set omero.db.name "$OMERO_DB_NAME"
OMERO.server/bin/omero config set omero.db.user "$OMERO_DB_USER"
OMERO.server/bin/omero config set omero.db.pass "$OMERO_DB_PASS"
OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"

but then...

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < OMERO.server/db.sql
-bash: OMERO.server/db.sql: No such file or directory

I've done a search for db.sql in the installation directory but can't find it. I am supposed to have downloaded the db.sql from somewhere else?

Thanks!

Stuart

Hi Stuart,

The community will needs some basics to be able to help you.

What reference are you using for the install? e.g. are you following one of the walkthroughs at e.g. https://www.openmicroscopy.org/site/sup ... index.html - and if so, which one?


What flavour or Linux are you installing to?
Is the server dedicated to OMERO?
Is it a physical machine or a VM?

Many thanks,

Kenny

Dear Kenny

Sorry for the late reply, I got seriously distracted by other urgent stuff!

I have a Scientific Linux 6 system (i.e. a RHEL 6 look-alike system) and I've been following https://www.openmicroscopy.org/site/sup ... ice36.html. The server will be dedicated to OMERO.

Regards

Stuart

Didn't you miss the step to generate DB script https://www.openmicroscopy.org/site/sup ... ero-server:

Code: Select all

OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS"

before

Code: Select all

psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < OMERO.server/db.sql

?

Ola

Hi Stuart,

sap1@york.ac.uk wrote:Sorry for the late reply, I got seriously distracted by other urgent stuff!

No problem!

If the server is to be dedicated to OMERO, would it be out of the question to upgrade to a newer operating system?

Running modern OMERO with any RHEL6 based OS can be tricker than it needs to be, keeping Python up to date in line with security patches.

We'd recommend CentOS 7 if you have a choice in the matter.

All the best,

Kenny

Dear Kenny

OK, I'll consider that option (I have a number of other servers thatI could use instead). However, the problem I am having is the non-existence of the db.sql file - where can I find it please?

Thanks

Stuart

Hi Stuart,

Did you see Ola's reply? It's a generated file, as she mentioned, generated by the command under the `Configure` step of the workflow you're following at https://www.openmicroscopy.org/site/sup ... ice36.html.

If you haven't created that file, the step must have been missed.

Best,

Kenny