SourceCode

Anonymous access to the latest hosted source code repositories

This page documents the process of obtaining anonymous CVS or RSYNC based access to the source code repositories hosted by the Open Bioinformatics Foundation. These methods are useful for obtaining cutting edge sourcecode and developer snapshots. Please visit the official Projects page for links to the project websites and downloads of official releases.

How to browse our latest source code repositories via the web

http://code.open-bio.org/cgi/viewcvs.cgi

Downloading and updating code via Anonymous CVS

• Make sure that CVS is installed on your system.
• Pick the repository that you wish to use

   * /home/repository/biopython
   * /home/repository/biojava
   * /home/repository/bioperl
   * /home/repository/biodas
   * /home/repository/moby
   * /home/repository/biocorba
   * /home/repository/biosql
   * /home/repository/bioruby
   * /home/repository/emboss
   * /home/repository/obf-common 

• Use the following command (all on one line) to login to the server. The example below shows how to login to the bioperl repository. To login to other repositories simply alter the /home/repository/(project) information.

   cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl login
   when prompted, the password is 'cvs'

• Each project CVS repository can have many different packages available for download. You may need to browse the web interface for a bit to determine the packages of interest. After a successful login you may "checkout" the project package you are interested in.

The following command should be executed as one line. The specific example shows how to check out the primary bioperl codebase which is contained in the "bioperl-live" package.

   cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl checkout bioperl-live

• The login and checkout procedure should only have to be done once. To update the source directories in the future it should be possible just to enter the top level directory and issue the following command:

   cvs update

Downloading and updating code via Anonymous RSYNC

The code.open-bio.org server also offers up read-only copies of source code repositories via anonymous rsync.

To see a list of available rsync modules, try this command:

 rsync rsync://code.open-bio.org

The server will echo back the list of configured repositories. The module name is appended to the "::" pattern to indicate to the rsync server that a module is being requested.

The following example shows how to obtain the latest Bioperl codebase snapshot using anonymous rsync:

 rsync -av code.open-bio.org::cvsbioperl .