Program:     music2 - Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.
Version:     V0.1
Author:      Beifang Niu && Cyriac Kandoth

Usage:  music2 <command> [options]

bmr                    ...  Calculate gene coverages and background mutation rates.
clinical-correlation        Correlate phenotypic traits against mutated genes, or       
                             against individual variants.
cosmic                      Match a list of variants to those in COSMIC, and highlight  
                             druggable targets.
cosmic-omim                 Compare the amino acid changes of supplied mutations to
                             COSMIC and OMIM databases.
create-visualizations       no description!!!: define doc in the class definition for
                             Genome::Model::Tools::Music::CreateVisualizations
data                   ...  Parse, standardize, and index various third-party datasets  
                             used by the tools in MuSiC.
mutation-relation           Identify relationships of mutation concurrency or mutual    
                             exclusivity in genes across cases.
path-scan                   Find signifcantly mutated pathways in a cohort given a list 
                             of somatic mutations.
pfam                        Add Pfam annotation to a MAF file.
play                        Run the full suite of MuSiC tools sequentially.
plot                   ...  Generate relevant plots and visualizations for MuSiC2.
proximity                   Perform a proximity analysis on a list of mutations.
proximity-window            Perform a sliding window proximity analysis on a list of mutations.
smg                         Identify significantly mutated genes.
survival                    Create survival plots and P-values for clinical and mutational phenotypes.      

    Install dependencies: 
       samtools    : http://sourceforge.net/projects/samtools
       joinx       : https://github.com/genome/joinx
       calcRoiCovg :https://github.com/Beifang/calcRoiCovg

    Install cpanm:
       http://search.cpan.org/~miyagawa/App-cpanminus-1.7001/bin/cpanm

    Just run: cpanm MuSiC2-0.1.tar.gz