cellorganizer-galaxy-tools

This repository contains the CellOrganizer Galaxy tools and the instructions on how to install them on your Galaxy instance.

CellOrganizer v2.8.1

Fixes

• Display shape space when dataset field is not present or empty.
• Generation of watertight SBML Spatial output has been corrected for translation errors.

Other

• The following models have been rebuilt using this version of CellOrganizer. Updated models can be found in the model repository.

  • 2D HeLa diffeomorphic framework
  • 2D HeLa PCA framework
  • 2D HeLa classic framework

• CellOrganizer for Galaxy now supports Galaxy server v19.05.

CellOrganizer v2.8.0

Features

• Added improved model for generating protein distributions during T cell synapse formation that only requires annotation of cell couples at a single time point model and improves synapse alignment. Includes training, synthesis and info demos.
• Added outline PCA model for 2D cell and nuclear shapes. Includes training, synthesis and info demos.
• Added SPHARM-RPDM model for 3D cell and nuclear shapes (see https://doi.org/10.1093/bioinformatics/bty983). Includes training, synthesis and info demos.

Fixes

• Fixed issues with options.train.flag. Valid options should be nuclear, cell, framework, and protein.

Enhancements

• Modularized and cleaned up img2slml.

Prerequisites

Before you attempt to install the tools make sure to have

• A working Galaxy instance. Installing Galaxy is beyond the scope of this document. Please refer to the official documentation to install an instance.

• Matlab. Matlab should be installed in the same machine running Galaxy. Installing Matlab is beyond the scope of this document. Please refer to the official documentation to build an instance.

• The Matlab binary must be in the $PATH of the user running Galaxy.

  For example

  ~ export PATH=$(PATH):/opt/matlab/bin  
  ~ echo $PATH
  /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/opt/matlab/bin
  
  ~ which matlab
  /opt/matlab/bin/matlab
  

Installing CellOrganizer for Galaxy

• CellOrganizer must be downloaded into the system running Galaxy. Its location should be set in an environment variable called $CELLORGANIZER. The environment variable needs to be accessible to the user running your Galaxy instance. Make sure the user running Galaxy has reading permissions on the CellOrganizer location.

  For example

  ~ chown -R galaxy:galaxy /usr15/galaxy/cellorganizer-galaxy-tools-v2.8.1/cellorganizer3
  ~ export CELLORGANIZER=/usr15/galaxy/cellorganizer-galaxy-tools-v2.8.1/cellorganizer3
  ~ echo $CELLORGANIZER
  /usr15/galaxy/cellorganizer-galaxy-tools-v2.8.1/cellorganizer3
  

  To download CellOrganizer visit the official website. Please make sure the version of CellOrganizer you install matches the version of CellOrganizer for Galaxy.

• Copy the CellOrganizer tools into the $GALAXY/tools. The variable $GALAXY, as explained in the official documentation, holds the location of your Galaxy instance.

Contributing

When contributing to this repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.

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Support for CellOrganizer has been provided by grants GM075205, GM090033 and GM103712 from the National Institute of General Medical Sciences, grants MCB1121919 and MCB1121793 from the U.S. National Science Foundation, by a Forschungspreis from the Alexander von Humboldt Foundation, and by the Freiburg Institute for Advanced Studies.

Copyright (c) 2007-2019 by the Murphy Lab at the Computational Biology Department in Carnegie Mellon University