README

CONTENTS AND COPYRIGHT

This directory contains the entire source tree for the
UCSC Genome Browser 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. Please see the LICENSE file in the
current directory for more details, the license differs by directory.
If you want only the MIT-licensed parts of the code (libraries and command
line tools, e.g. for use in package managers and pipelines), have a look at
https://github.com/ucscGenomeBrowser/kent-core

Commercial users interested in the UCSC Genome Browser please see
    http://genome.ucsc.edu/license/.
    https://genome-store.ucsc.edu/
Commercial users interested in BLAT, gfServer, isPCR and related tools should
contact http://www.kentinformatics.com/ for access

If you want to run a local installation of the UCSC Genome Browser
(we call this a mirror, even when it includes only a small
part of the data), you do not need the whole source tree. We provide
statically compiled binary CGI-bin executables, the apache htdocs folder,
binary MySQL databases and ancillary large data files in /gbdb via an Rsync
download server.  For install details see
    http://genome.ucsc.edu/admin/mirror.html

The pre-compiled user application binaries may function on your system
without this build procedure.  For example to obtain the
linux.x86_64 binaries:
 rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./

Mac OSX binaries available via:
 rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/ ./

If you are looking for only the MIT licensed, minimal part of the source code
to build the command line tools, e.g. for pipelines and package managers, see
this code repository: https://github.com/ucscGenomeBrowser/kent-core
 
Most source code users will only be interested in the kent/src/inc and
kent/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 kent/src/hg/hgTracks.

The current version number is stored in src/hg/inc/versionInfo.h .
The current version of a running genome browser is displayed in the html
tag <TITLE> by the hgTracks program, e.g. http://genome.ucsc.edu/cgi-bin/hgTracks, 
in modern internet browsers, hover over a tab to show it.

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:
     rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/jksrc.zip ./
     or:
     wget --timestamping http://hgdownload.soe.ucsc.edu/admin/jksrc.zip
   The unzip result from that file will establish a directory hierarchy:
     ./kent/...

2. Run make:

     cd src
     make utils

   Usually, the locations of the required libraries on your system are auto-detected.

SEE ALSO: http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads
          https://genome-store.ucsc.edu/
          http://genome.ucsc.edu/goldenPath/help/mirror.html#manual-installation-instructions
          http://genome.ucsc.edu/goldenPath/help/mirrorManual.html#building-the-kent-source-tree

INSTALL INSTRUCTIONS FOR BLAT

1. Follow the general install instructions above.
3. Execute make in each of the following directories:
     kent/src/gfServer
     kent/src/gfClient
     kent/src/blat
     kent/src/utils/faToNib

INSTALL INSTRUCTIONS FOR A LOCAL GENOME BROWSER MIRROR (a mirror can have only some assemblies)

   In most cases, you will not need to modify the source code to install a
   Genome Browser webserver locally.

   Overview https://genome.ucsc.edu/goldenPath/help/mirror.html
   Manual installation https://genome.ucsc.edu/goldenPath/help/mirrorManual.html
   TrackDb documentation https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html
   Rare TrackDb statements kent/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 kent/src/README in particular should be read by anyone modifying
   the C source code.