Genome Browser Git Access

Access Browser Code Using Git

Install Git:
Install Git software version 1.6.2.2 or later. See the Git Community Handbook installation and setup instructions, as well as our Installing git Genomewiki page.

Start an initial Git local repository:

$ git clone git://genome-source.soe.ucsc.edu/kent.git

Or, if a firewall prevents git daemon port 9418, use:

$ git clone http://genome-source.soe.ucsc.edu/kent.git

The kent source tree will be imported to the current working directory in a directory named ./kent/.

Track the beta branch at UCSC repository:
Most users want to use the beta branch, which has tested, released versions of the browser. To create a beta tracking branch:

$ cd kent
$ git checkout -t -b beta origin/beta

The -b creates a local branch with the name "beta", and checks it out.
The -t makes it a tracking branch, so that "git pull" pulls in updates from origin/beta, the "real" beta branch in our public central read-only repository.

To get the latest UCSC release:
Type this command From anywhere within the kent source tree:

$ git pull

To view the source via gitlist:
Browse to http://genome-source.soe.ucsc.edu/gitlist/.

To construct a permanent URL to our source code files:
1. Boilerplate URL base:

http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/

2. Add the path/file to the end:

src/makefile

Example:

http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/makefile

Updates:
UCSC generally updates the origin/beta branch every three weeks. If you are updating database tables for a mirror site, we recommend that you update the source at the same time, as source code is sometimes modified to include operations on new columns that have been added to database tables.

See also: the README files in the source tree directory src/product/README.*. For instructions on keeping local tracks separate from UCSC Genome Browser tracks, see src/product/README.trackDb.

For comments or questions, contact genome-mirror@cse.ucsc.edu.