This is a Perl interface to the UCSC Genome Browser BigWig and BigBed
files, which are indexed genome feature databases that can be randomly
accessed across the network. Please see
http://genome.ucsc.edu/FAQ/FAQformat.html for information about
creating these files.

To compile this module, you must first download, unpack and compile
the Jim Kent source tree, located at
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip. Please follow the
instructions contained in the source tree to create the main library
file jkweb.a

This module will prompt you for the location of the Kent source tree
the first time you build it. This should be the "src" directory which
contains the subdirectories "inc" and "lib". If you do not wish to be
prompted, set the environment variable KENT_SRC to point to the
directory.

You will also need to install a recent version of Bio::Perl from CPAN.

Then run:

  perl Build.PL
  ./Build
  ./Build test
  (sudo) ./Build install

MAC OSX ISSUES:

On Mac OSX platforms prior to Snow Leopard you may encounter the
following fatal error when building this module:

   Symbol not found: _environ

This is due to a problem in the Macintosh header files that causes one
of the Kent sources to compile incorrectly.

If you encounter this problem, then do the following:

 1) cd to the "src" subdirectory of the Kent source tree. This is the directory
     that contains the "lib" and "inc" directories.

 2) run the command:

     patch < -p1 < /path/to/Bio-BigFile-1.XX/patches/kent_src_patch_macosx.diff

 3) Rerun "make" in the Kent source tree

 4) Rerun "./Build" in the Bio-BigFile directory.

TROUBLESHOOTING:

If you encounter problems during compiling, you may need to set the
environment variable MACHTYPE to point to the appropriate architecture
for your system. This is described in the installation directions for
the Jim Kent source tree.

AUTHOR: 

Lincoln D. Stein <lincoln.stein@gmail.com>

Copyright (c) 2010 Ontario Institute for Cancer Research

This package and its accompanying libraries are free software; you can
redistribute the package and/or modify it under the terms of the GPL
(either version 1, or at your option, any later version) or the
Artistic License 2.0.  Refer to LICENSE for the full license text.
