OMERO.server installation¶

package

$ sudo apt-get update

$ sudo apt-get install package

$ which java
/usr/bin/java
$ java -version
openjdk version "11.0.5" 2019-10-15
OpenJDK Runtime Environment (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04)
OpenJDK 64-Bit Server VM (build 11.0.5+10-post-Ubuntu-0ubuntu1.118.04, mixed mode, sharing)

$ python3 --version
Python 3.6.4

$ mkdir -p ~/omero

$ cd ~/omero

$ unzip OMERO.server-5.6.0-ice36-byy.zip
$ ln -s OMERO.server-5.6.0-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

$ omero config set omero.db.name 'omero_database'
$ omero config set omero.db.user 'db_user'
$ omero config set omero.db.pass 'db_password'

$ omero config get

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

$ 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
$ omero admin diagnostics

$ 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

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

$ omero admin diagnostics

================================================================================
OMERO Diagnostics 5.6.0
================================================================================

Commands:   java -version                  11.0.5    (/usr/bin/java)
Commands:   python -V                      3.6.9     (/opt/omero/server/venv3/bin/python)
Commands:   icegridnode --version          3.6.5     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.5     (/usr/bin/icegridadmin)
Commands:   psql --version                 11.6      (/usr/bin/psql)
Commands:   openssl version                1.1.111   (/usr/bin/openssl)

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:    /opt/omero/server/OMERO.server/var/log exists

Log files:  Blitz-0.log                    22.8 KB        errors=0    warnings=9
Log files:  DropBox.log                    1.3 KB        errors=0    warnings=1
Log files:  FileServer.log                 114 B
Log files:  Indexer-0.log                  1.3 KB       errors=0    warnings=5
Log files:  MonitorServer.log              882 B
Log files:  PixelData-0.log                1.8 KB        errors=0    warnings=4
Log files:  Processor-0.log                592 B        errors=0    warnings=1
Log files:  Tables-0.log                   841 B
Log files:  TestDropBox.log                n/a
Log files:  master.err                     34.4 KB        errors=2    warnings=0
Log files:  master.out                     empty
Log files:  Total size                     0.06 MB

Environment:OMERODIR=/opt/omero/server/OMERO.server
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/opt/omero/server/venv3/bin:/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-server/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

System	Package
Debian	openjdk-11-jre
Homebrew	N/A (install Oracle Java)
RedHat	java-11-openjdk

System	Package
Debian	python3
Homebrew	python3
RedHat	python3

System	Package
Debian	mencoder
Homebrew	mplayer
RedHat	mencoder

System	Package
Debian	unzip
Homebrew	unzip
RedHat	unzip

OMERO.server installation¶

Prerequisites¶

Java SE Runtime Environment (JRE)¶

Python 3¶

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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