UCSC Computational Biology CVS Source Repository

A CVS repository has been established to assist in the development of UCSC's computational biology software. For those who are not familiar with CVS, a great deal of documentation is referenced on this page. Anyone wanting assistance with using CVS with existing modules or adding new modules to the repository should contact Mark Diekhans.

Repository Location

The CVS repository is located in:

    /projects/compbio/cvsroot

You should either set the CVSROOT environment variable to point to this directory or specified on the CVS command line

    cvs -d /projects/compbio/cvsroot

when checking out modules.

Compbio Modules

The following modules are currently in the repository:

SAM - Sequence Alignment and Modeling System.
CVSPlay - Test module for those wanting to learn CVS. Feel free to add, modify, or delete files in this module.
CompbioCVSDoc - This set of HTML pages; CVS documentation collected for the compbio group.
measure_shift - Tools to score the similarity of two alignments based on residue shifting.

CVS - Concurrent Versions System

CVS is a "Source Control" or "Revision Control" tool designed to keep track of source changes made by groups of developers working on the same files, allowing them to stay in sync with each other as each individual chooses.

One of the key features of CVS is that checked out files are not locked, instead conflicts are resolved when modified files are checked back into the repository. This eliminates the problem of a development being blocked because another user has a file locked.

CVS Documentation:

CVS Primer
CVS Tutorial (somewhat outdated)
CVS Reference Manual:
- HTML format
- GNU info format: /usr/local/gnu/info/cvs.info
The CVS FAQ
CVS Bubbles (Pointers to CVS information)
Just ask...

Use the CVSPlay module to experiment with CVS.