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Making the USCS toolkit for Windows

UCSC provide a whole set of binary tools for file viewing and manipulation:

These include

  • wigToBigWig
  • samtools

The problem is that these are not available for Windows. However, they can be built using cygwin. The source should be downloaded from

It is suggested that this is only done for 64 bit machines using the cygwin 64bit toolchain as many of the tools will be unusable within a 32 bit address space.

The default build includes debug info (-g) and does not do a full optimisation (-O2). To override, the code should be built using

make CFLAGS=-O3 COPT=-O3

Some additional cygwin modules may well be required in order to build the code, particularly:

  • libmysqld-devel
  • libpng-devel

The mysql should pull in the zlib library which is also required. If it does not then there does not appear to be a 64bit cygwin zlib library, but loading the zlib-devel source, building it and then moving libz.a to /lib should fix the problem.