Cytoscape installation fails without warning

[GoogleCodeExporter]

What steps will reproduce the problem(s)?
1. Download AltAnalyze for a machine running Windows and install a species 
database. Cytoscape will be downloaded and extracted automatically. However, 
Cytoscape will prompt will either simply fail to open or prompt an 
incompatibility warning (32bit or 64bit incompatibility).
2. Download AltAnalyze for a machine running OSX and install a species 
database. Cytoscape will be downloaded and extracted automatically. However, 
Cytoscape will fail to open when the Cytoscape.app is selected without warning. 
Only opening it in a terminal window with the command "./Cytoscape.app" or 
opening the .jar file will initiate Cytoscape.

Cause of the error:
(Windows) After the cytoscape.zip file is downloaded, zip extraction creates 
faulty binary files due to an apparent problem with Python's builtin zipfile 
library.
(Mac) Unlike Windows, zipfile propperly extracts the cytoscape.zip download, 
however, permissions on the directories cause restricted access to files, 
unless permissions are changed (chmod -R 777 directory).

Solution in next release:
(all operating systems) The Cytoscape folder will be distributed as a 
cytoscape.gz.tar file which is extracted properly by the AltAnalyze supported 
extraction methods. Cytoscape was shown to run properly when extracted from 
this file.
(Mac) Permissions on the Cytoscape directory have been changed. 

Original issue reported on code.google.com by nsalomo...@gmail.com on 26 Mar 2011 at 6:49

[GoogleCodeExporter]

I'll handle this one.

Original comment by nsalomo...@gmail.com on 5 Jul 2012 at 9:14

[nsalomonis]

Note: Cytoscape integration no longer supported in AltAnalyze version 2+