deepTools 1.5.3

Useful library to deal with mapped reads in sorted BAM format.

deepTools: suite of common processing routies for deep sequencing data

This suite of tools provides useful routines to deal with mapped reads. This includes converting bams to bigwig or bedgraph coverage files, run a GC correction and plot heatmaps and profiles.

Install from source

The easiest way to install deepTools is by downloading the source file and using python pip or easy_install tools:

$ pip install deepTools $ vim [deepTools folder]/config/deepTools.cfg

The deepTools.cfg file contains several variables that need to be adjusted.

Other option is to clone the repository

$ git clone https://github.com/fidelram/deepTools

Then go to the deepTools directory, edit the deepTools.cfg file and then run the install script a:

$ cd deepTools $ vim config/deepTools.cfg $ python setup.py install

By default, the script will install python library and executable codes globally, which means you need to be root or administrator of the machine to complete the installation. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script.

$ python setup.py --help

To install under a specific location use:

$ python setup.py install --prefix <target directory>