CONTENTS AND COPYRIGHT

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 [email protected] 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.  
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
   the scope of this README).  The default MACHTYPE is often a
   long string: "i386-redhat-linux-gnu"
   which will not function correctly in this build environment.
   It needs to be something simple such as one of:
	i386 i686 sparc alpha x86_64 ppc etc ...
   with no other alpha characters such as: -
   To determine what your system reports itself as, try the
   uname options:  'uname -m' or 'uname -p' or 'uname -a'
   on your command line.  If necessary set this environment variable.
   Do this under the bash shell as so:
       MACHTYPE=something
       export MACHTYPE
   or under tcsh as so:
       setenv MACHTYPE something
   and place this setting in your home directory .bashrc or .tcshrc
   environment files so it will be set properly the next time you
   login.  Remember to "export" it as show here for the bash shell.
3. Make the directory ~/bin/$MACHTYPE which is
   where the (non-web) executables will go.
   Add this directory to your path.
4. Go to the src/lib directory.  If it doesn't
   already exist do a mkdir $MACHTYPE.
5. Type make.  On Alphas there will be 
   some warning messages about "crudeAli.c"
   otherwise it should compile cleanly.
   It's using gcc.
6. Go to src/jkOwnLib and type make.
7. Go to the application you want to make and type 
   make.  (If you're not sure, as a simple test
   go to src/utils/fixcr and type make,
   then 'rehash' if necessary so your shell
   can find the fixcr program in ~/bin/$(MACHTYPE).
   The fixcr program changes Microsoft style
   <CR><LF> line terminations to Unix style
   <LF> terminations.  Look at the "gotCr.c"
   file in the fixCr directory, and then
   do a "fixcr gotCr.c" on it.


INSTALL INSTRUCTIONS FOR BLAT

1. Follow the general install instructions above.
2. If you're on an alpha system do a:
     setenv SOCKETLIB -lxnet
   on Solaris do
     setenv SOCKETLIB "-lsocket -lnsl"
   on SunOS do
     setenv SOCKETLIB "-lsocket -lnsl -lresolv"
   on Linux you can skip this step.
3. Execute make in each of the following directories:
     src/gfServer
     src/gfClient
     src/blat
     src/utils/faToNib

INSTALL INSTRUCTIONS FOR CODE USING THE BROWSER DATABASE
(and other code in the src/hg subdirectory)

1. Follow the general install instructions above.
2. Make the environment variable MYSQLINC point to
   where MySQL's include files are.  (On my
   system they are at /usr/include/mysql.)
   While you're at it set the MYSQLLIBS
   variable to point to something like
   /usr/lib/mysql/libmysqlclient.a -lz
   When available, the commands: mysql_config --include
	and mysql_config --libs
	will display the required arguments for these environment settings.
3. Execute make in src/hg/lib
4. Execute make in the directory containing the
   application you wish to build.
5. See also: http://genome.ucsc.edu/admin/jk-install.html
   and more documentation in this source tree about setting up
   a working browser in README files:
       src/product/README.building.source
       src/product/README.local.git.source
       src/product/README.mysql.setup
       src/product/README.install
       src/product/README.trackDb
       src/hg/makeDb/trackDb/README
   There are numerous README files in the source tree describing
   functions or modules in that area of the source tree.
   The src/README in particular should be read by anyone modifying
   the C source code, and python/README by anyone modifying the Python.