SourceCode

The following OBF supported projects originally used CVS and/or SVN hosted by the OBF, but are now using git hosted on [github.com]:

   * BioRuby uses http://github.com/bioruby/bioruby
   * Biopython uses http://github.com/biopython/biopython
   * BioPerl uses http://github.com/bioperl
   * BioSQL uses http://github.com/biosql/biosql

Anonymous access to the latest hosted source code repositories

This page documents the process of obtaining anonymous CVS, SVN 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:

Note to casual users

The methods described here grant access to live snapshots of our current code repositories. The files may be in constant flux and certainly do not reflect official packages and supported releases.

For downloads of tested and released software, please visit the official Projects page for links to the project websites and download locations.

Note to developers

This page describes methods for obtaining read only access to the latest snapshots of our source code. Updates, fixes and new code can not be committed or uploaded using the methods described here. The exceptions are BioRuby and Biopython, which can be forked on github (allowing you to modify you own personal repository).

How to browse our latest source code repositories via the web

Projects using CVS repositories: http://code.open-bio.org/cgi/viewcvs.cgi

Projects using Subversion repositories: http://code.open-bio.org/svnweb/

Downloading and updating code via Anonymous CVS

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

IMPORTANT NOTE (Starting in 2008): BioPerl and BioJava are switching from CVS to Subversion for source code version control management. At some point the CVS links below for BioPerl and BioJava will be removed.

   * /home/repository/biopython obsolete, now using git.
   * /home/repository/biojava obsolete, now using SVN, see here
   * /home/repository/bioperl obsolete, now using git.
   * /home/repository/biodas
   * /home/repository/moby
   * /home/repository/biocorba
   * /home/repository/biosql obsolete, now using git.
   * /home/repository/bioruby obsolete, now using git.
   * /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 .

Downloading and updating code via Anonymous SVN

The code.open-bio.org server also offers up read-only copies of source code repositories via anonymous SVN. A list of code repositories available via SVN can be seen here: http://code.open-bio.org/svnweb/index.cgi

Example Usage:

To see what SVN modules the BioJava project is making available, try this command:

 svn list svn://code.open-bio.org/biojava

The following example shows how to obtain the latest Bioperl codebase snapshot using anonymous SVN, it will check out the latest copy of bioperl-live/ from the "SVN trunk" and will locally store it in a directory named "bioperl-live" on your system:

 svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live

Troubleshooting Anonymous SVN

If you encounter an error while using the SVN client or SVN Web interface, the likely cause is that our server is in the middle of replicating the repository from the primary source. While the mirror and replication process occurs, it is not unusual for SVN client functionality to break temporarily.

The final step of our codebase replication process is to explicitly re-verify the health and status of each repository, this process takes a few moments but while it occurs the repository is "locked" and unavailable for access.

• Anonymous SVN repositories are updated/mirrored hourly from the primary developer server
• Anonymous SVN repositories are verified and repaired (if necessary) every 20 minutes

If a SVN client error occurs for longer than 20 minutes, please report this to: support@helpdesk.open-bio.org