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README.md

OMERO User Scripts

Installation

  1. Change into the scripts location of your OMERO installation

     cd OMERO_DIST/lib/scripts
    
  2. Clone the repository with a unique name (e.g. "useful_scripts")

     git clone https://github.com/THISREPOSITORY/omero-user-scripts.git UNIQUE_NAME
    
  3. Update your list of installed scripts by examining the list of scripts in OMERO.insight or OMERO.web, or by running the following command

     path/to/bin/omero script list
    

Upgrading

  1. Change into the repository location cloned into during installation

     cd OMERO_DIST/lib/scripts/UNIQUE_NAME
    
  2. Update the repository to the latest version

     git pull --rebase
    
  3. Update your list of installed scripts by examining the list of scripts in OMERO.insight or OMERO.web, or by running the following command

     path/to/bin/omero script list
    

Developer Installation

  1. Fork omero-user-scripts in your own GitHub account

  2. Change into the scripts location of your OMERO installation

     cd OMERO_DIST/lib/scripts
    
  3. Clone the repository

     git clone git@github.com:YOURGITUSER/omero-user-scripts.git YOUR_SCRIPTS
    

Adding a script

  1. Choose a naming scheme for your scripts. The name of the clone (e.g. "YOUR_SCRIPTS"), the script name, and all sub-directories will be shown to your users in the UI, so think about script organization upfront.

    a. If you don't plan to have many scripts, then you need not have any sub-directories and can place scripts directly under YOUR_SCRIPTS.

    b. Otherwise, create a suitable sub-directory. Examples of directories in use can be found in the official scripts repository.

  2. Place your script in the chosen directory:

  • If you have an existing script, simply save it.
  • Otherwise, copy Example.txt and edit it in place. (Don't use git mv)
  1. Add the file to git, commit, and push.

Testing your script

  1. List the current scripts in the system

     path/to/bin/omero script list
    
  2. List the parameters

     path/to/bin/omero script params SCRIPT_ID
    
  3. Launch the script

     path/to/bin/omero script launch SCRIPT_ID
    
  4. See the developer documentation for more information on testing and modifying your scripts.

Legal

See LICENSE

About

This section provides machine-readable information about your scripts. It will be used to help generate a landing page and links for your work. Please modify all values on each branch to describe your scripts.

Repository name

Base OMERO User Scripts repository

Minimum version

4.4

Maximum version

4.4

Owner(s)

Pierre Pouchin

Institution

Génétique, Reproduction et Développement

URL

https://github.com/ppouchin/omero-user-scripts

Email

pierre.pouchin@udamail.fr

Description
  • Check_original.py allows users to check which files from the DropBox folder have not been imported, but it's only useful for users belonging to 1 group.
  • Rename_images.py allows users to batch rename images (remove the path to the DropBox folder for example). Regular expressions are not supported though.
  • Restore_colors.py fixes the colors (LUT) for LIF and LSM files in some cases where the colors were not correctly imported.
  • Restore_date.py was made to fix "acquisition date" based on file stats when it did not work properly. It may be obsolete now...
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