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 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.