LOCKER: cytoscape FILE: /mit/cytoscape/README.athena CONTENTS: Cytoscape base locker DESCRIPTION: Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. HOW TO RUN: add cytoscape runcyto FROM DASH: no INTERFACES: GUI VERSIONS: For Linux 32/64: Cytoscape 3.3.0, 3.5.1 DEPENDENCIES: Java 8 runtime DATAFILES: Platform-independent LICENSE SERVER: no ------------------------------------------------------------------------- SUPPORT ISSUES -- I/S SUPPORT: CONSULTING: none TRAINING: none DOCUMENTATION: internal help system, local manual at http://web.mit.edu/cytoscape_v3.5.1/Cytoscape3_5_0Manual.pdf OTHER SUPPORT: author documentation at http://www.cytoscape.org/documentation_users.html CONSULTING: (none) TRAINING: tutorials at http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3 DOCUMENTATION: WEB PAGE: http://www.cytoscape.org/ BUG REPORTS: Use sendbug ------------------------------------------------------------------------- LEGAL ISSUES -- STATUS: freely distributable- licensed under LGPL. See http://www.cytoscape.org/download.php for details SITES: any RESTRICTIONS: DOCUMENTATION: licensed under the Creative Commons license, 2006. ------------------------------------------------------------------------- ABOUT THIS LOCKER -- MAINTAINER(S): swmaint (group), alexp DIRECTORY STRUCTURE: arch - arch hierarchy current - link to current version cytoscape_v3.3.0 - link to version 3.3.0 cytoscape_v3.5.1 - link to version 3.5.1 MODIFY HISTORY: 1/7/14 - Alex Prengel Created this README.athena, initial locker setup 3/30/16 - Alex Prengel Installed 3.3.0, set it as default 5/25/17 - Alex Prengel Installed 3.5.1, set it as default MISCELLANEOUS: Cytoscape was designed to be installed locally on user's machines, and in particular was not designed to run out of network file systems such as AFS. This presents challenges in our environment, where we have to install it in AFS. The local launch script runcyto was tailored to work around a variety of issues: Cytoscape expects to find a configuration directory CytoscapeConfiguration in each user's home directory; the contents are typically quite large, at least 300 megabytes and possibly significantly more. This directory is also accessed frequently while Cytoscape is running, and this would cause Cytoscape to run extremely slowly if it were located in AFS. For these reasons we cache it in /var/tmp while Cytoscape is running, and save it in compressed form in the user's home directory, in file cyto302sav.tar.gz, when it is not. (CytoscapeConfiguration in the user's home directory is a symlink to the cache location). Users will thus encounter two "please wait..." messages during a run, once before Cytoscape launch (while the script is populating the cache), and once after program termination (while the script is repacking the cache files for storage in the user's home directory). It is very important to allow both these operations to complete if you want to preserve the state of your configuration; for the same reason, you shouldn't delete file cyto302sav.tar.gz or the CytoscapeConfiguration link in your home directory (if you do, the launch script will recreate these in a default configuration). Unfortunately this can take a bit of time- on a reasonably fast computer with good network connectivity each of these operations takes about a minute or two. Due to the large size of the CytoscapeConfiguration directory, there are various situations where you may run out of disk quota, in your initial setup or on repackaging the cache for storage- the size can increase significantly during a run, especially if you install any of the add-on packages. The script will check for these situations, and will alert you to extra space needed if you have an AFS home directory (the Athena default). If you don't have an AFS home directory all this checking is skipped, and the CytoscapeConfiguration directory is just installed within your home directory as per the program's expectation. Given the above, users shouldn't run more than one instance of Cytoscape at a time. Also, Cytoscape won't run on the Athena dialups due to memory issues. As a consequence of the installation directory being read-only to users, you may see an error message like the following at launch: Unable to update instance pid: /afs/athena.mit.edu/software/cytoscape_v3.5.1/fra mework/instances/instance.properties (Permission denied) As far as we can determine, this is harmless.