056e69e891aeedd0c826cb2652ec8535955977bb kent Fri Apr 6 16:18:00 2012 -0700 Adding more information about source tree structure and revisiting list of useful library modules. diff --git README README index 0cb3a55..8a2d088 100644 --- README +++ README @@ -2,33 +2,32 @@ This directory contains the entire source tree for the UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs as well as some of Jim Kent's own tools. All files are copyrighted, but license is hereby granted for personal, academic, and non-profit use. A license is also granted for the contents of the src/lib, src/inc and src/utils and python directories for commercial users. Commercial users should contact kent@soe.ucsc.edu for access to other modules. Commercial users interested in the UCSC Genome Browser in particular please see http://genome.ucsc.edu/license/. Most source code users will only be interested in the src/inc and src/lib directories, which contain the interfaces and implementations to the library routines, and in a few specific applications. -The applications are scattered in other directories. -Many of them are web based. A few of them expect -the MySQL database to be around. +The applications are scattered in other directories. Many of them are web based. +The UCSC Genome Browser in particular is mostly found in src/hg/hgTracks. GENERAL INSTALL INSTRUCTIONS 1. Get the code. The best way to do this now for Unix users is via Git following the instructions at: http://genome.ucsc.edu/admin/git.html Or, fetch the entire source in a single file: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip Note further documentation for the build process in your unpacked source tree in src/product/README.* Especially note README.building.source and the "Known problems" for typical situations you may encounter. 2. Check that the environment variable MACHTYPE exists on your system. It should exist on Unix/Linux. (And making this on non-Unix systems is beyond