Open Microscopy Environment

Hi All,

My department has been talking about OMERO for ages and essentially wants an OMERO Server setup and working but no of us have a clue where to start. I've had a play a few times of the last year but always get stuck at some point so thought I'd hold out my hand and see if any of you kind people could help me along the way?

I happy to go with any config you suggest but have been playing with CentOS 7 and Ice 3.6.

All went well until this bit which gave me errors and I didn't understand why if its a problem so I skipped it.

pip install -r `dirname $0`/requirements.txt

and also "Create a database user and initialize a new database for OMERO:" always goes wrong but as Im just copy and pasting the commands from the instructions page perhaps I should be modifying them in some way.

I'd appreciate any help at all.

Many thanks in advanced.

tintin wrote:I happy to go with any config you suggest but have been playing with CentOS 7 and Ice 3.6.

This sounds generally fine. Which version of OMERO are you trying to install?

All went well until this bit which gave me errors and I didn't understand why if its a problem so I skipped it.

pip install -r `dirname $0`/requirements.txt

Sorry about that. It's been an issue for others recently: https://trello.com/c/BAOre90k/171-bugs

See https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=8113 for more info.

and also "Create a database user and initialize a new database for OMERO:" always goes wrong but as Im just copy and pasting the commands from the instructions page perhaps I should be modifying them in some way.

Can you point to which step you're on in the documentation and what your error message is?

Hope we can help.
~Josh.

Thanks for your fast response Josh.

"This sounds generally fine. Which version of OMERO are you trying to install?"

I don't think I every got as far as to choose which version but I honestly don't mind so whatever you suggest.

"Sorry about that. It's been an issue for others recently: https://trello.com/c/BAOre90k/171-bugs

See viewtopic.php?f=5&t=8113 for more info."

Thanks for that.

"Can you point to which step you're on in the documentation and what your error message is?"

I copy and paste the below commands:

echo "CREATE USER $OMERO_DB_USER PASSWORD '$OMERO_DB_PASS'" | \
su - postgres -c psql

su - postgres -c "createdb -E UTF8 -O '$OMERO_DB_USER' '$OMERO_DB_NAME'"

psql -P pager=off -h localhost -U "$OMERO_DB_USER" -l

but after this last one I get a prompt to enter the password for user. I've tried $OMERO_DB_PASS & DB_PASS but both give me the below response.

Password for user :
psql: FATAL: password authentication failed for user "root"
[root@CentOS omero]#

I also tried the root password but that gives me the same message.

Thanks again for you offer of help.

tintin wrote:psql -P pager=off -h localhost -U "$OMERO_DB_USER" -l

but after this last one I get a prompt to enter the password for user. I've tried $OMERO_DB_PASS & DB_PASS but both give me the below response.

Password for user :
psql: FATAL: password authentication failed for user "root"
[root@CentOS omero]#

I also tried the root password but that gives me the same message.

This sounds like the "To install PostgreSQL 9.4:" step may not have worked correctly. Can you share your /var/lib/pgsql/9.4/data/pg_hba.conf file?

Cheers,
~Josh

Hi Josh,

Its not letting me upload a .conf file as an attachment on the forum.

Any ideas?

Sorry

You can either zip it or paste the last dozen lines or so in a code block here.

Cheers,
~Josh.

Ok its zipped. Many thanks again for all your time.

Your pg_hba.conf looks ok. Perhaps then you are having the same issues as seen in https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8163.

It will likely be best for you to simplify the commands removing quotes & environment variables using the values you expect to work. E.g.

Code: Select all

echo "CREATE USER omero somepassword" | \
     su - postgres -c psql

su - postgres -c "createdb -E UTF8 -O omero omero"

psql -P pager=off -h localhost -U omero -l


(entering somepassword when asked)

Cheers,
~Josh.

Hi there, I'm encountering the same problems (or at least very similar). The last suggestion did not work for me:

echo "CREATE USER omero somepassword" | su - postgres -c psql

results in an "unrecognized role option "somepassword"

Anything I've done wrong here? I thought I followed the instruction line-by-line ?

THanks,
Olaf

PS: following the "OMERO.server installation on CentOS 7 and Ice 3.6" instructions

Hi Olaf,
I think Josh missed a keyword there:

Code: Select all

echo "CREATE USER omero PASSWORD 'yourpassword'" | su - postgres -c psql


Cheers,

Will.