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INSTALL.md

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OMERO.csvtools installation

Minimum requirements

  • OMERO.server 5.0
  • Java 6
  • Python 2.6
  • GNU bash

Package overview

The toolset contains three subcomponents:

  • omero-csv-tools-<VERSION>.jar: the Java tool - may be invoked as a standalone utility or via its companion scripts
  • Csv_Annotation_Tool.py: the OMERO.scripts tool - may be invoked from script-aware OMERO clients, and relies on a companion script/command to launch the Java tool
  • csv-annotation-tool-script.sh: the companion shell script - acts as an executable wrapper/glu around the Java tool

In order to ensure compatibility between the OMERO.server and the client Blitz libraries bundled with the toolset, it is recommended to select OMERO_FLAVORs with matching major OMERO versions for download (eg. 'ome50x' for the '5.0.x' server line).

OMERO.csvtools deployment as an OMERO.script

Get the standalone distribution

  • Download omero-csv-tools-<VERSION>-<OMERO_FLAVOR>-standalone.zip

  • Unpack to a location of your choice.

Example - assuming deployment to /opt/OMERO.csvtools:

mkdir -p /opt/OMERO.csvtools
unzip omero-csv-tools-<VERSION>-dist-standalone.zip -d /opt/OMERO.csvtools

Configure the server scripting environment

  • Deploy the OMERO scripts located in the scripts/omero/annotation_scripts distribution folder to your OMERO server: add the annotation_scripts directory to your OMERO.server/lib/scripts/omero/ directory. Alternatively, you may wish to upload the script with the built-in OMERO command line utilities:

    cd /opt/OMERO.csvtools/scripts $OMERO_PREFIX/bin/omero script upload -u root --official omero/annotation_scripts/Csv_Annotation_Tool.py

  • Check that the companion shell script bin/csv-annotation-tool-script.sh is executable for the OMERO user, or chmod u+x bin/csv-annotation-tool-script.sh

  • Make sure the companion shell script is available on the PATH environment variable - hence accessible to the OMERO.server scripting environment: export PATH=$PATH:/opt/OMERO.csvtools/omero-csv-annotation-tool/bin. Alternatively, you may wish to keep the PATH unchanged and edit Csv_Annotation_Tool.py prior to upload such that csv-annotation-tool-script.sh is referenced via its absolute path: COMMAND_NAME = "/opt/OMERO.csvtools/bin/csv-annotation-tool-script.sh"

Run the script

  • Upload a CSV file as an attachment to an OMERO project or dataset.

  • Launch the script from OMERO.server, OMERO.insight or OMERO.web via Scripts > Annotation Scripts > CSV Annotation Tool.

OMERO.csvtools deployment as a standalone CLI tool

  • As above, unpack the distribution (either standalone or with dependencies).

  • Run cd bin && ./csv-annotation-tool-cli.sh for usage arguments.

Miscellaneous

Alternate deployment options

Two binary distributions are supplied:

  • standalone: contains all the required classpath dependencies bundled into a single jar file (ie. uberjar distribution).

  • with dependencies: provides all required classpath dependencies as individual jars.

Depending on your needs and preferences, you may choose either: the standalone distribution allows deployment from a single package, whereas using separate dependencies provides a more fine grained classpath management (eg. cherry-picking jars and shell scripts to a different location such as OMERO.server/lib and OMERO.server/bin, or overriding the Blitz libraries versions bundled with the tool).

## Operating system support

The "full toolset" (ie. Java tool + companion scripts) is currently unsupported on Windows environments.

Some subcomponents would require adjusting to enable Windows support:

  • the Java tool should work out of the box as a CLI-only OMERO client
  • the OMERO.scripts tool should work provided the COMMAND_NAME is edited accordingly
  • the companion shell script would require porting to a native command interpreter, or inlining into the python OMERO script

Reference documentation