Below are some instructions that may help get TGI's MuSiC suite of tools installed on various Linux distributions. But please keep in mind that we cannot test, troubleshoot, and package MuSiC on too many distributions because of the complex dependencies. And this is why we officially support only Ubuntu.
For the latest officially supported installation instructions, please visit this page.
Update (9/26/2016): Users familiar with docker should quit while you're ahead, and pull this image, based on the Ding lab's most recent MuSiC2. And this here is a better documented docker image based on the first release of MuSiC (v0.4.1)
Important: These step-by-step instructions tested successfully on the latest releases of these OSes as of Feb 2, 2013. If you are using a different version, or a different OS, then you will likely encounter error messages from a compiler, package manager, or cpanm. To minimize the noise on this thread, please do not post your error messages if you are not familiar with compiling code, handling dependencies, or CPAN. But after you've taught yourself a bit, with a little googling, please do post your solutions (as answers to this post) or fixes (as comments). Or suggest ways to generalize these instructions, so I won't have to update them as often. ;)
For Fedora, CentOS6 or RHEL6 users
Make sure you have access to EPEL, a repository with some packages we'll need:
sudo rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
sudo yum update -y
Install some packaged prerequisites, and their nested dependencies:
sudo yum install -y curl gcc make perl git samtools samtools-devel BEDTools R-core R-devel perl-devel expat-devel zlib-devel
Download and build tabix, and move it where locally compiled packages reside:
git clone https://github.com/samtools/tabix.git
cd tabix
make
sudo mv tabix bgzip /usr/local/bin/
Follow the latest online instructions to build and install joinx: https://github.com/genome/joinx
For Debian or Ubuntu users
Install some packaged prerequisites, and their nested dependencies:
sudo apt-get install curl gcc make perl git samtools libbam-dev bedtools r-base-core libexpat1-dev zlib1g-dev tabix
Download the latest joinx stable release, solve some build dependencies, and then build and install it:
git clone --recursive https://github.com/genome/joinx.git
sudo apt-get install build-essential cmake libbz2-dev libgtest-dev
cd joinx;
git checkout v1.6.17;
mkdir build; cd build
cmake .. -DCMAKE_BUILD_TYPE=release
make deps
make
sudo make install
For all users
Download and build calcRoiCovg, and move it where locally compiled packages reside:
curl -LO https://github.com/samtools/samtools/archive/0.1.19.tar.gz
tar -zxf 0.1.19.tar.gz
export SAMDIR=$PWD/samtools-0.1.19
cd samtools-0.1.19
make
cd ..
git clone https://github.com/ding-lab/calc-roi-covg.git
cd calc-roi-covg
make
sudo mv calcRoiCovg /usr/local/bin/
Install some R packages that enable parallelization across cores:
curl -LO "http://cran.r-project.org/src/contrib/Archive/{multicore/multicore_0.2.tar.gz,iterators/iterators_1.0.7.tar.gz,foreach/foreach_1.4.2.tar.gz,doMC/doMC_1.3.3.tar.gz}"
sudo R CMD INSTALL multicore_0.2.tar.gz iterators_1.0.7.tar.gz foreach_1.4.2.tar.gz doMC_1.3.3.tar.gz
Download and install cpanminus (cpanm), for simpler installation of Perl modules:
curl -L http://cpanmin.us | sudo perl - --self-upgrade
Install some prerequisite Perl modules:
sudo `which cpanm` -n Text::CSV_XS Statistics::Distributions Statistics::Descriptive PDL PDL::Stats Module::Build Regexp::Common Time::HiRes IPC::Cmd LWP::Simple List::MoreUtils Set::Scalar Bit::Vector UR
sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome/genome_0.80.1-3.tar.gz
Install MuSiC:
sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-music/genome-music_0.4.1-1.tar.gz
You should now be able to list all of MuSiC's available sub-commands using:
genome music --help
Datafiles and sample inputs
The datafiles used by MuSiC's cosmic-omim and pfam tools are downloadable from here. Sample ROI files for use with bmr calc-covg and bmr calc-bmr, can be found in the calc-roi-covg repo, and sample MAF files can be downloaded from the TCGA (but you should read this post first). If you don't have access to BAM files for bmr calc-covg, then you can use UCSC wiggle track files with bmr calc-wig-covg instead, downloadable from Broad's Firehose (look for tarballs containing the words "Mutation_Packager_Coverage")
Nice job, thanks for this.
FYI there is a more recent docker available at https://github.com/readline/docker/tree/master/MuSiC , however it's outdated and it doesnt work.
I made my own version of this and committed it back to dockerhub
Will get the fully installed GenomeMUSIC to try out. I dont maintain this software just trying to help people get to use it.
Note that the lab has since released a MuSiC2, which is also dockerized here.
"`which cpanm`" is not required, "cpanm" is enough (bash will resolve this automatically)
Note that installation of genome-1.80.1-3 fails on any machine with more than a single - (dash) in it's hostname.
I just tried on a server called xxxx-yyyy-head-node.fully.qual.domain.com and got this error:
I then tried it on a server with two dashes in it's hostname:
When I hand edit the code to get around this problem, the next issue I face is the following. This is all done on Centos 7 with cpan -l . "filename".
Hi Cyriac, Could you please provide a link to download the KEGG file in the format accepted by Music/Music2.
thanks !