Note: This page is only useful to Cytoscape core developers who have secure access that allows them to modify

Instructions for updating

  1. Check out the cyto_web directory from Subversion.
    • Note: do a clean check out periodically to make sure temporary files that build up on your local copy are not copied to the website. Also, directories may be added, which would not be checked out with an update.
    • The command is:
      • svn co svn+ssh:// cyto_web
  2. Only modify content in this directory instead of directly on Remember to test and commit your changes. This allows us to collaboratively edit the website without overwriting other people's changes.
  3. When you are done editing, deploy the changes to the website (see below)

Deploying to

To deploy web site changes to, from your workstation:

  1. You need to set up a public/private SSH key pair to access the website.

    1. You can do this by going to Contact Mike Smoot or another Cytoscape developer for the login and password.

    2. Once logged in, click on the "Secure Shell" icon and then add your public key. Beware of spaces when you copy your key!
    3. Once your keys are correctly configured you should be ready to deploy.
  2. You need to have Apache ant installed and available from the command line (test by typing 'ant' on the command line and seeing if it is found).
  3. Run the script to deploy
    1. On Mac OS X or Linux, type: (preferred method)

        This does two things:
        1. runs ant config_prod, so that everything is set up for production.
        2. runs rsync to incrementally and securely update
          rsync is much more efficent and secure than FTP. So this is the preferred way to do deployments.

    2. On Windows, type:
      • ant deploy -Dpassword=[value]

        Where [value] is replaced with the actual password This does two things:

        1. runs ant config_prod, so that everything is set up for production.
        2. copies files over via the ant FTP task. This is slow, so the prefered way to deploy is from a unix based operating system using rsync, above.

Note: you can also use any FTP or SCP client to post files. This might be useful for changes to single files - just make sure the file is in CVS or it will be overwritten next time someone uses the deploy script. (last edited 2009-02-12 01:03:15 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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