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README

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.

Step 1) COMPILE JIM KENT SOURCE TREE

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. The commands needed to
get, unpack and compile the necessary file are:

 wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
 unzip jksrc.zip
 cd kent/src/lib
 export    MACHTYPE=i686    # for a 64-bit system
 # export  MACHTYPE=i386    # for a 32-bit system
 make
 cd ..
 export KENT_SRC=`pwd`

Step 2) INSTALL BIO::PERL

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

  perl -MCPAN -e 'install Bio::Perl'

Step 3) COMPILE BIO::DB::BIGWIG

From within this directory, run:

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

If you did not define the environment KENT_SRC in step 1, the "perl
Build.PL" step will prompt you for the location of the Kent source
tree. Please provide 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 this directory.

 ** ISSUES AND TROUBLESHOOTING **

PROBLEM 1) Compilation fails with a "relocation error" or warnings about
recompiling with "-fPIC".

Some combinations of Perl, GCC and jksrc do not play well together. If
you see warnings like these, you will need to patch and recompile the
kent source. Find the file kent/src/inc/common.mk and modify the
following line:

 Old:
  CFLAGS=
     
 New:
  CFLAGS=-fPIC

Then run make again from within kent/src/lib

PROBLEM 2) On Mac OSX systems, compilation fails with "Symbol not found: _environ"

This occurs on Mac OSX platforms prior to Snow Leopard. It 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.

PROBLEM 3) Compilation of the Kent surce fails.

If you encounter errors while compiling the Kent source, 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.
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