Install OMERO 4.1 on Mac OS X 10.5
This walkthrough is a list of the commands used to install OMERO on a clean Mac OS 10.5 Leopard by manually downloading and configuring the required components.
It is not a substitute for the general install page but is here to give a feel for the process.
Prerequisites
On a completely clean machine the first step is to install Xcode from Apple http://developer.apple.com/TOOLS/.
Starting with the basics, you need a text editor. I downloaded TextWrangler from http://www.barebones.com/products/TextWrangler/.
You also need Java (at least 1.5), which comes as standard on OS X 10.5.
PostgreSQL 8.3
I downloaded PostgreSQL from here I went for PostgreSQL 8.4 BUT this required editing some trust configuration to allow access!?! MUCH easier to download PostgreSQL 8.3, which is still available. To add the PostgreSQL to the PATH, you need to edit the profile of the bash shell (Terminal).
In TextWrangler?, go to File > "Open Hidden" and look in your home directory /User/will for the .bash_profile file. If it is not there, create a new file and add this line (edited to your equivalent location).
export PATH=$PATH:/Library/PostgreSQL/8.4/bin/
Then save this file in your home directory.
ICE
Now for ICE. I went to the ice download page and got the Ice-3.3.1-bin-macosx.tar.gz under Binary Archive: MacOS X (Intel x86) Archive. I unzipped the file and put the folder on my Desktop.
Now I need to move it into the /opt/ directory. I needed to create this as it didn't exist. See if it's there.
ten-five-eight-2009-08-06:~ will$ cd ../../
ten-five-eight-2009-08-06:/ will$ ls -al
drwxr-xr-x 3 will admin 102 19 Oct 12:13 opt
If it's not in the listed folders create it, then move the Ice folder into opt
ten-five-eight-2009-08-06:/ will$ mkdir /opt
ten-five-eight-2009-08-06:/ will$ cd Users/will/
ten-five-eight-2009-08-06:~ will$ mv Desktop/Ice-3.3.1/ /opt
Now you need to edit the .bash_profile again, to include the various components of Ice. Add these lines to the .bash_profile, editing the location of your Ice directory as appropriate in the first line:
export ICE_HOME=/opt/Ice-3.3.1
export PATH=$PATH:$ICE_HOME/bin
export PYTHONPATH=$ICE_HOME/python:$PYTHONPATH
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$ICE_HOME/lib
Python
Now, check you have Python (and what version) by typing python:
ten-five-eight-2009-08-06:~ will$ python
Python 2.5.1 (r251:54863, Jun 17 2009, 20:37:34)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> ^D
ten-five-eight-2009-08-06:~ will$
Python Imaging Library, Matplotlib (numpy, mencoder etc)
These Python components are not required for the majority of OMERO server and client functionality, so they can be omitted if you want a simpler install process. The Python Imaging Library (PIL) is used for creating Figures for export (e.g. exporting movie) and Matplotlib is used for some charts (server usage figure) on the web client. Matplotlib requires numpy, which will also be needed for the PyTables functionality currently being developed.
I installed PIL using these instructions, downloading from here.
To get matplotlib, go to their web-site and click the download button, which takes you here. I downloaded the matplotlib-0.99.1.1-py2.5-macosx10.5.dmg and installed from there.
For the movie export to work, you need the mencoder command installed. Follow the instructions for Mac on the movie page. I unzipped the mencoder.zip in my Downloads folder, then moved it to usr/local/bin:
sudo mv /Users/will/Downloads/mencoder /usr/local/bin/mencoder
OMERO
I downloaded the server, moved the folder to Desktop and renamed it omero.
Followed the database configuration steps as described. In this case I used the "default" names suggested on the install page for user: "omero" and database name "omero". However, I chose a different password, using "ome" instead of "omero". This means I have to configure this later.
ten-five-eight-2009-08-06:~ will$ sudo -u postgres createuser -P -D -R -S omero
Enter password for new role:
Enter it again:
ten-five-eight-2009-08-06:~ will$ sudo -u postgres createdb -O omero omero
ten-five-eight-2009-08-06:~ will$ sudo -u postgres createlang plpgsql omero
createlang: language "plpgsql" is already installed in database "omero"
ten-five-eight-2009-08-06:~ will$ psql -h localhost -U omero -l
Password for user omero:
List of databases
Name | Owner | Encoding | Collation | Ctype | Access privileges
-----------+----------+----------+-----------+-------+-----------------------
omero | omero | UTF8 | C | C |
postgres | postgres | UTF8 | C | C |
template0 | postgres | UTF8 | C | C | =c/postgres
: postgres=CTc/postgres
template1 | postgres | UTF8 | C | C | =c/postgres
: postgres=CTc/postgres
(4 rows)
Made the /OMERO directory (as root), then allow the regular user to write to it.
ten-five-eight-2009-08-06:~ will$ sudo mkdir /OMERO
ten-five-eight-2009-08-06:~ will$ whoami
will
ten-five-eight-2009-08-06:~ will$ sudo chown -R will /OMERO
Now edit any configurations for connecting to the database. As described above, I used the default "omero" for user name and database name, but chose "ome" as my password. Therefore I need change into the Desktop/omero directory and run the password configuration:
ten-five-eight-2009-08-06:~ will$ cd Desktop/omero
ten-five-eight-2009-08-06:omero will$ bin/omero config set omero.db.pass ome
Then set-up the db as described:
ten-five-eight-2009-08-06:omero will$ bin/omero db script
Please enter omero.db.version [OMERO4.1]:
Please enter omero.db.patch [0]:
Please enter password for OMERO root user:
Please re-enter password for OMERO root user:
Saving to /Users/will/Desktop/omero/OMERO4.1__0.sql
ten-five-eight-2009-08-06:omero will$
Then enter the location of the .sql (see last line above) in the next command, to create the database:
psql -h localhost -U omero omero < OMERO4.1__0.sql
Now START the server!
bin/omero admin start
I had a few things not work the first time (hadn't set-up database permissions with bin/omero config set omero.db.pass TopSecret?) so I had to stop the server with bin/omero admin stop , fix the problem and then restart. NB. If you stop the server, sometimes you have to wait a minute before restarting.
At this point, you should be able to download the OMERO clients and log in using the 'root' username and password you specified above at the prompt: "Please enter password for OMERO root user:".
OMERO.web
If you want to use the web-client to connect to the server or the web-admin to add new users, read on...
NB. The instructions have changed for OMERO 4.1.1 (see the install page). The following instructions are for 4.1.0.
I edited the PYTHONPATH as instructed (by adding this line to .bash_profile)
export PYTHONPATH=$PYTHONPATH:~/Desktop/omero/lib/python/
so my PYTHONPATH is now....
ten-five-eight-2009-08-06:~ will$ echo $PYTHONPATH
/opt/Ice-3.3.1/python::/Users/will/Desktop/omero/lib/python/
Now I'm going to follow the settings instructions. I am using the current IP of this computer from System Preferences > Sharing > Web sharing (on).
ten-five-eight-2009-08-06:omero will$ bin/omero web settings
You just installed OMERO, which means you didn't have settings configured in OMERO.web.
Please enter the domain you want to run OMERO.web on (http://www.domain.com:8000/)http://10.12.2.40:8000/
Please enter the Email address you want to send from (omero_admin@example.com): will@dundee.ac.uk
Please enter the SMTP server host you want to send from (smtp.example.com): smtp.dundee.ac.uk
Optional: please enter the SMTP server port (default 25):
Optional: Please enter the SMTP server username: wmoore
Optional: Password:
Optional: TSL? (yes/no): no
Saving to /Users/will/Desktop/omero/lib/python/omeroweb/custom_settings.py
ten-five-eight-2009-08-06:omero will$
Same with superuser
ten-five-eight-2009-08-06:omero will$ bin/omero web superuser
Please enter Username for OMERO.web administrator: ome
Please enter Email address: will@lifesci.dundee.ac.uk
Please enter password for OMERO.web administrator:
Please re-enter password for OMERO.web administrator:
Saving to /Users/will/Desktop/omero/lib/python/omeroweb/initial_data.json
ten-five-eight-2009-08-06:omero will$ bin/omero web syncdb
Database synchronization...
Creating table django_admin_log
.
.
Installing json fixture 'initial_data' from absolute path.
Installed 7 object(s) from 1 fixture(s)
OMERO.web was prepared. Please start the application.
ten-five-eight-2009-08-06:omero will$
Now enabled and started web
ten-five-eight-2009-08-06:omero will$ bin/omero admin ice
Ice 3.3.1 Copyright 2003-2009 ZeroC, Inc.
>>> server enable Web
>>> server start Web
>>> exit
And at this point I was able to go to the localhost on this machine and log in as root user at http://localhost:8000/webclient/
I still needed to configure the IP so that other machines can connect to the web-client. Following instructions to edit the three files as described, I opened them for editing in TextWrangler:
ten-five-eight-2009-08-06:omero will$ edit etc/grid/default.xml
ten-five-eight-2009-08-06:omero will$ edit etc/grid/templates.xml
ten-five-eight-2009-08-06:omero will$ edit lib/python/omero/plugins/server.py
I stopped web server as described and started it again. Can now connect from other machines to this one, using http://10.12.2.40:8000/webclient
You can now go to http://localhost:8000/webclient (or http://10.12.2.40:8000/webclient from another machine) and create Scientist (user) accounts, remembering to check the "Active" checkbox.
