Pre-reqs ======== Server (or vm) built is to standard "CentOS-6-x86_64-MIN" cat /etc/redhar-release: CentOS release 6.5 (Final)" Create the YUM repository: epel-x86_64.repo postgres: install: yum install postgresql <- postgresql-8.4.20-1.el6_5.x86_64 yum install postgresql-server <- postgresql-server-8.4.20-1.el6_5.x86_64 Initiate and then start postgres: service postgresql initdb service postgresql start vi /var/lib/pgsql/data/pg_hba.conf and amend the following lines: host all all 127.0.0.1/32 ident host all all ::1/128 ident to host all all 127.0.0.1/32 md5 host all all ::1/128 md5 service postgresql restart chkconfig postgresql on Java yum install java-1.7.0 <- java-1.7.0-openjdk-1.7.0.55-2.4.7.1.el6_5.x86_64 Ice: Download the following from: http://www.zeroc.com/download/Ice/3.5/Ice-3.5.1-el6-x86_64-rpm.tar.gz tar -xvf Ice-3.5.1-el6-x86_64-rpm.tar.gz Install: yum localinstall --nogpgcheck mcpp-* yum localinstall --nogpgcheck db53* yum localinstall --nogpgcheck ice-* python-devel yum install python-devel <- python-devel-2.6.6-52.el6.x86_64 Python Imaging yum install python-imaging <- python-imaging-1.1.6-19.el6.x86_64 C language (required for Numpy) Install: yum install gcc <- gcc-4.4.7-4.el6.x86_64 yum install gcc-c++ <- gcc-c++-4.4.7-4.el6.x86_64 Numpy Download tar.gz file from: <- numpy-1.8.1.tar.gz http://sourceforge.net/projects/numpy/files/NumPy/ Install: tar -xvf numpy.tar.file; cd numpy* python setup.py build python setup.py install freetype-devel: yum install freetype-devel <- freetype-devel-2.3.11-14.el6_3.1.x86_64 libpng-devel: yum install libpng-devel <- libpng-devel-1.2.49-1.el6_2.x86_64 matplotlib: Download an older tar.gz file <- matplotlib-1.2.1.tar.gz The latest version tries to download an update file, but this server has no external network connection! Download from: http://matplotlib.org/downloads.html Install: tar -xvf matplotlib.tar.file; cd maplotlib-1.2.1 python setup.py build python setup.py install numexpr: Download the tar.gz file from <- numexpr-2.1.tar.gz https://code.google.com/p/numexpr/ Install: tar -xvf numexpr-tar.file ; cd numexpr* python setup.py build python setup.py install Cython: Download the the tar.gz file from <- Cython-0.20.2.tar.gz http://cython.org/#download Install: tar -xvf Cython-0.20.1.tar.gz ; cd Cython* python setup.py build python setup.py install hdf5: Download the tar.gz from <- hdf5-1.8.13.tar.gz http://www.hdfgroup.org/HDF5/ (follow links to http://www.hdfgroup.org/ftp/HDF5/current/) Install: tar -xvf hdf5-1.8.12.tar.gz ; cd hdf5* ./configure --prefix=/usr/hdf5 make; make install export HDF5_DIR=/usr/hdf5 pytables: Download the tar.gz from <- tables-3.1.1.tar.gz http://sourceforge.net/projects/pytables/files/pytables/ Install: tar -xvf tables-tarfile.tar.gz ; cd tables* python setup.py build --hdf5=/usr/hdf5 python setup.py install --hdf5=/usr/hdf5 gfortran yum install gcc-gfortran <- gcc-gfortran-4.4.7-4.el6.x86_64 atlas: yum install atlas atlas-devel <- atlas-3.8.4-2.el6.x86_64 <- atlas-devel-3.8.4-2.el6.x86_64 scipy: Download the tar.gz from <-scipy-0.14.0.tar.gz http://sourceforge.net/projects/scipy/files/scipy/ Install: tar -xvf scipy.tar.file ; cd scipy* python setup.py build python setup.py install Python Setuptools: yum install python-setuptools <- python-setuptools-0.6.10-3.el6.noarch Pillow: Download the zip file from <- Pillow-2.4.0.zip https://pypi.python.org/pypi/Pillow Install: unzip pillow.zip.file ; cd pillow python setup.py build python setup.py install Ommero: ======= Download Omero from: http://www.openmicroscopy.org/site/support/omero4 Unpack Omero: unzip OMERO.server-version.zip Create an Omero user and create directory sudo mkdir /OMERO groupadd omero (check group is 8889 in /etc/groups). useradd -d /home/omero -m -g 8889 omero (make sure user is 8889 in /etc/passwd). sudo chown -R omero:omero /OMERO/ Create an Omero database: sudo -u postgres createuser -P -D -R -S omero sudo -u postgres createdb -O omero --encoding=SQL_ASCII --template=template0 omero sudo -u postgres createlang plpgsql omero psql -h localhost -U omero -l Move the Omero source to /opt and change its owner: mv OMERO_direcory /opt/OMERO_directory chown -R omero:omero /opt/OMERO_directory ln -s /opt/OMERO_directory /opt/Omero Install and login as the omero user: su - omero cd /opt/Omero bin/omero config set omero.db.name 'omero' bin/omero config set omero.db.user 'omero' bin/omero config set omero.db.pass bin/omero db script psql -h localhost -U omero omero < OMEROx.x__0.sql export DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/hdf5:/usr/hdf5/lib export LD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/hdf5:/usr/hdf5/lib export OMERO_PREFIX=/opt/Omero export ICE_HOME=/usr/share/Ice-3.5.1 export JAVA_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64 export JRE_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64 export PATH=$PATH:$JAVA_HOME:$OMERO_PREFIX/bin export OMERO_HOME=/opt/Omero edit /opt/Omero/etc/omero.properties Update the db name, user and password: omero.db.name=omero omero.db.user=omero omero.db.pass= bin/omero admin diagnostics bin/omero admin start bin/omero login Attempt to connect to the server using Omero Client application (OMERO.insight). IP address will be server IP address, port will be: 4064. The user name will be "root", and the password will be whatever you used. OMERO.web ========= As root: service httpd start su - omero export DYLD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/hdf5:/usr/hdf5/lib export LD_LIBRARY_PATH=/usr/share/java:/usr/lib/:/usr/hdf5:/usr/hdf5/lib export OMERO_PREFIX=/opt/Omero export ICE_HOME=/usr/share/Ice-3.5.1 export JAVA_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64 export JRE_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64 export PATH=$PATH:$JAVA_HOME:$OMERO_PREFIX/bin export OMERO_HOME=/opt/Omero cd /opt/Omero bin/omero config set omero.web.application_server 'fastcgi-tcp' bin/omero web config apache <-- Add the resulting stanza to /etc/httpd/conf/httpd.conf (as root) Also add the following line to /etc/httpd/conf/httpd.conf: Alias / "/opt/Omero/var/omero.fcgi/" In order to enable httpd server to user fastCGI: as root: yum install httpd-devel.x86_64 apr-devel.x86_64 Download mod_fastcgi rpm from rpm.pbone.net yum localinstall --nogpgcheck mod_fastcgi rpm The fastcgi was difficult to get working. In the end I also used: as omero user: bin/omero config set omero.web.application_host "http://149.155.xxx.xxx" bin/omero web syncmedia And I disabled the upgrade_check by updating the "upgrade_check.py" script to return without doing the check. This was because just setting it to "" (as per the guidance from Omero website) did not disable the check! vi /opt/Omero/lib/python/omero/util/upgrade_check.py Find "disabled" in the file, and add a "return;", as follows: # If None or empty, the upgrade check is disabled. if self.url == None or len(self.url) == 0: return; # EARLY EXIT! return; Check the fastcgi.conf file in /etc/httpd/conf.d vi /etc/httpd/conf.d/fastcgi.conf This file should contain ONLy the following line uncommented: LoadModule fastcgi_module modules/mod_fastcgi.so Start (or restart) HTTPD: service httpd restart Once all done, try and restart Omero and Omero.web and try to log on with the web interface: bin/omero web stop bin/omero admin stop bin/omero admin start bin/omero web start