OMERO.server installation¶

package

$ sudo apt-get update

$ sudo apt-get install package

$ which java
/usr/bin/java
$ java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

$ python --version
Python 2.7.10

$ mkdir -p ~/omero

$ cd ~/omero

$ unzip OMERO.server-5.4.2-ice36-byy.zip

$ ln -s OMERO.server-5.4.2-ice36-byy OMERO.server

Username: db_user
Password: db_password
Database: omero_database

$ sudo -u postgres createuser -P -D -R -S db_user
Enter password for new role:       # db_password
Enter it again:       # db_password

$ sudo -u postgres createdb -E UTF8 -O db_user omero_database

$ psql -h localhost -U db_user -l
Password for user db_user:
        List of databases
   Name         |  Owner   | Encoding
----------------+----------+-----------
 omero_database | db_user  | UTF8
 postgres       | postgres | UTF8
 template0      | postgres | UTF8
 template1      | postgres | UTF8
(4 rows)

$ sudo mkdir /OMERO

$ whoami
omero
$ sudo chown -R omero /OMERO

$ cd ~/omero/OMERO.server
$ bin/omero config set omero.db.name 'omero_database'
$ bin/omero config set omero.db.user 'db_user'
$ bin/omero config set omero.db.pass 'db_password'

$ cd ~/omero/OMERO.server
$ bin/omero config get

$ omero config set omero.data.dir /srv/omero

$ cd ~/omero/OMERO.server
$ bin/omero db script --password omero_root_password

Using OMERO5.4 for version
Using 0 for patch
Using password from commandline
Saving to /home/omero/OMERO5.4__0.sql

$ psql -h localhost -U db_user omero_database < OMERO5.4__0.sql

$ bin/omero admin diagnostics

$ bin/omero admin start
Creating var/master
Initializing var/log
Creating var/registry
No descriptor given. Using etc/grid/default.xml

$ chmod 700 ~/omero/OMERO.server/etc ~/omero/OMERO.server/var

$ bin/omero login
Server: [localhost]
Username: [root]
Password:         # omero_root_password

$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.4.2
================================================================================

Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.7.9     (/usr/bin/python)
Commands:   icegridnode --version          3.6.3     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.3     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.4.5    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 30324, enabled)
Server:     DropBox                        active (pid = 30343, enabled)
Server:     FileServer                     active (pid = 30345, enabled)
Server:     Indexer-0                      active (pid = 30348, enabled)
Server:     MonitorServer                  active (pid = 30351, enabled)
Server:     OMERO.Glacier2                 active (pid = 30353, enabled)
Server:     OMERO.IceStorm                 active (pid = 30376, enabled)
Server:     PixelData-0                    active (pid = 30393, enabled)
Server:     Processor-0                    active (pid = 30394, enabled)
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

OMERO:      SSL port                       4064
OMERO:      TCP port                       4063

Log dir:    /home/omero/OMERO.server-5.0.1-ice35-b21/var/log exists

Log files:  Blitz-0.log                    3.0 MB        errors=0    warnings=9
Log files:  DropBox.log                    4.0 KB        errors=0    warnings=1
Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  10.0 KB       errors=0    warnings=5
Log files:  MonitorServer.log              2.0 KB
Log files:  OMEROweb.log                   642.0 KB      errors=0    warnings=1
Log files:  OMEROweb_request.log           0.0 KB
Log files:  PixelData-0.log                7.0 KB        errors=0    warnings=4
Log files:  Processor-0.log                2.0 KB        errors=0    warnings=1
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB        errors=2    warnings=0
Log files:  master.out                     0.0 KB
Log files:  Total size                     3.83 MB

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir: '/OMERO'        Exists? True    Is writable? True
OMERO temp dir: '/home/omero/tmp'        Exists? True    Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 16952)
Django version: 1.8.7

System	Package
BSD Ports	java/openjdk7
Debian	openjdk-7-jre
Homebrew	N/A (install Oracle Java)
RedHat	java-1.8.0-openjdk

Package	Functionality	Downloads
NumPy (1.2.0 or higher)	Scripting	Numpy/Scipy page
PyTables (2.1.0 or higher) [1]	OMERO.tables	PyTables page

System	Package
BSD Ports	lang/python27 math/py-numpy devel/py-tables
Debian	python2.7 python-numpy python-tables
Homebrew	python numpy
RedHat	python

System	Packages
BSD Ports	multimedia/mencoder
Debian	mencoder
Homebrew	mplayer
RedHat	mencoder

System	Package
BSD Ports	archivers/unzip
Debian	unzip
Homebrew	unzip
RedHat	unzip

OMERO.server installation¶

Prerequisites¶

Java SE Runtime Environment (JRE)¶

Python 2¶

Ice¶

OMERO.scripts¶

Installation¶

Server directory¶

OMERO.server¶

Environment variables¶

Creating a database¶

Location for the your OMERO binary repository¶

Configuration¶

JVM memory settings¶

Enabling movie creation from OMERO.¶

Post-installation items¶

Backup¶

Security¶

Advanced configuration¶

Troubleshooting¶

OMERO diagnostics¶

Update notification¶

Page Contents

OMERO

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