I think I forgot to mention that you need the command plug-in installed. You can find it here: http://apps.cytoscape.org/apps/commandtool (also through the Plugin Manager in Cytoscape).

Give it a try. This plugin will also add a command console, accessible through the plugins menu, where you can experiment with commands. For example, try opening the command console and typing “help network”.

–
Martijn

Thanks a lot for your post.
I have problems replicating your example.
I’m using everything as posted by you, except the line
‘vizmap import file=net.props’
which I deleted from the script.

I’m using:
Cytoscape_v2.6.3
Ubuntu 11.04

This is the content of my cytoscape.sh file:
java -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar cytoscape.CyMain -p plugins “$@”

Here is the output:

$./cytoscape.sh -S cyto_script
cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu
cytoscape[INFO]: starting delete action
cytoscape[INFO]: ending delete action
cytoscape[INFO]: PreferenceAction()…
cytoscape.actions.BookmarkAction[INFO]: BookmarkAction()…
BatchTool initializing
BatchTool: args = cytoscape.CyMain -p plugins -S cyto_script
Opening file cyto_script
Processing script file cyto_script
Parsing exception: Unknown command: network

(and at this point Cytoscape GUI remains open but no network is loaded)

I would appreciate your help on this regard.

One more thing, supposing I get the script to work, is it possible to use another command line in the script for saving the network generated in graphic format (PDF, PNG, etc) ?

Best regards,

Manuel