biofer / MuSiC2

identifying mutational significance in cancer genomes

MuSiC2

Mutational Significance in Cancer (Cancer Mutation Analysis) version 2.

Usage

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

Usage:  music2 <command> [options]

Key commands:

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 (Ubuntu 14.04.01)

Prerequisites:

Install samtools ( Download the samtools-0.1.19 from SOURCEFORGE (http://sourceforge.net/projects/samtools/files/samtools/0.1.19) )

    tar jxf samtools-0.1.19.tar.bz2
    cd samtools-0.1.19
    make
    export SAMDIR=$PWD
    sudo mv samtools /usr/local/bin/

Install joinx

    git clone --recursive https://github.com/genome/joinx.git
    sudo apt-get install build-essential cmake libbz2-dev libgtest-dev
    cd joinx
    mkdir build
    cd build
    cmake .. -DCMAKE_BUILD_TYPE=release
    make deps
    make
    sudo make install

Install calcRoiCovg

    sudo apt-get install git libbam-dev zlib1g-dev
    git clone https://github.com/Beifang/calcRoiCovg.git
    cd calc-roi-covg
    make
    sudo mv calcRoiCovg /usr/local/bin/

Install bedtools

    curl http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz > BEDTools.tar.gz
    tar -zxvf BEDTools.tar.gz
    cd BEDTools-v2.17.0
    make
    sudo mv ./bin /usr/local/bin/

In order to install MuSiC2 package, we need CPANM program (cpanm - get, unpack build and install modules from CPANM)

    sudo apt-get install cpanminus

Intall Perl5 local lib

    cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)

Intall Test::Most module

    wget http://search.cpan.org/CPAN/authors/id/O/OV/OVID/Test-Most-0.34.tar.gz
    cpanm Test-Most-0.34.tar.gz

Intall Statistics::Descriptive module cpanm Statistics::Descriptive cpanm Statistics::Distributions

Install MuSiC2 package

    git clone https://github.com/ding-lab/MuSiC2
    cd MuSiC2
    cpanm MuSiC2-#.#.tar.gz

example

SUPPORT

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