[Next-Generation Sequencing Book]
  • [Photo] J.W. Bizzaro • February 9, 2006
    We're pleased to announce another addition to the services offered to bioinformatic developers at Bioinformatics.Org. Effective immediately, developers may use the Subversion (SVN) version control system on our servers. Subversion was developed "to take over the CVS user base," according to the Subversion website. "Specifically, we're writing a new version control system that is very similar to CVS, but fixes many things that are broken." Here are a few of the advantages of using Subversion over CVS (from the website):
    • Directories, renames, and file meta-data are versioned.
    Lack of these features is one of the most common complaints against CVS. Subversion versions not only file contents and file existence, but also directories, copies, and renames. It also allows arbitrary metadata ("properties") to be versioned along with any file or directory, andprovides a mechanism for versioning the `execute' permission flag on files.
    • Commits are truly atomic.
    No part of a commit takes effect until the entire commit has succeeded. Revision numbers are per-commit, not per-file; log messages are attached to the revision, not stored redundantly as in CVS.
    • Versioning of symbolic links
    Unix users can place symbolic links under version control. The links are recreated in Unix working copies, but not in win32 working copies.
    • Efficient handling of binary files
    Subversion is equally efficient on binary as on text files, because it uses a binary diffing algorithm to transmit and store successive revisions.

    Subversion at Bioinformatics.Org makes use of svnserve over SSH for developer access (anonymous access uses ordinary svnserve). Instructions on using Subversion at BiO can be found here:
    http://bioinformatics.org/docs/svn/

    We also have the WebSVN interface set up:
    http://bioinformatics.org/websvn/

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