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 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.