Installation

Requirements for installation of dspchip

Requirements

dspchip has been implemented in Python, hence you will need this :-)

There is a number of libraries you should install as dependencies:

• numpy
• scipy, backbode for most of the processing
• pywt, for wavelet denoising
• pysam, for reading BAM files
• matplotlib, for plotting issues
• bx-python, for handy readers of wig and interval files

Also, you will beed bigWigInfo, bigWigToBedGraph and wigToBigWig executables to support bigWig file format (until I have native python support). If you can't build from source, there are precompiled versions here

Installation

Install the dependencies above, then get the source (either the tarball or the svn source). Unpack the archive and issue:

$ python setup.py build
$ sudo python setup.py install

within the archive directory. Follow python distutils instruction for additional options, i.e.

$ python setup.py --help-commands

or

$ python setup.py install --help