Bioinformatics for Cancer Genomics Copy Number Analysis Lab 2015

Workshop pages for students

Lab Module 5 - Software Installation Instructions

This page describes where to get and how to install the software used for this lab module.

Installing Array Normalization Packages

We will use the procedure described on the penncnv site. This page also contains links to most of the software we need to download.

Note: You will need to register with Affymetrix to download the library files, specifically the .cdf file, from the affimetrix site. The aroma-project has a copy available which we will download since it can be done from the cloud.

wget http://www.openbioinformatics.org/penncnv/download/penncnv.latest.tar.gz
tar -xzvf penncnv.latest.tar.gz

wget http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz
tar -xzvf gw6.tar.gz
wget http://media.affymetrix.com/Download/updates/apt-1.17.0-x86_64-intel-linux.zip
unzip apt-1.17.0-x86_64-intel-linux.zip
wget http://www.aroma-project.org/data/annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6.cdf.gz
gunzip GenomeWideSNP_6.cdf.gz

Installing OncoSNP

For predicting CNVs from the array data we will use OncoSNP in this lab. The files for OncoSNP can be downloaded from https://sites.google.com/site/oncosnp/user-guide/downloads. Before you can use OncoSNP, you will need to register with the author and he will supply a password which you can use to unlock the downloaded files.

Here we will download OncoSNP version 1.4:

wget http://www.well.ox.ac.uk/~cyau/oncosnp/oncosnp_v1.4.run
bash oncosnp_v1.4.run          # enter your oncosnp password

Then follow the on-screen instructions.

You’ll also need to get the matching MATLAB MCR file to be used with OncoSNP. This will be described on the website.

wget ftp://ftp.stats.ox.ac.uk/pub/yau/oncosnp/mcr/MCRinstaller.run.zip
unzip MCRinstaller.run.zip
bash MCRinstaller.run          # enter your oncosnp password, and select installation directory

The MCRinstaller.run installer will ask you where to install the MATLAB MCR files. You should export MCR_DIR= to create an environment variable pointing to the location to which you installed MATLAB MCR. The MCR will be located in a subdirectory MATLAB_Compiler_Runtime/vXXX for version XXX of the compiler.

We will also need to download GC content files for the relevant build of the genome. For this tutorial we will use the hg19 (build 37) files.

wget ftp://ftp.stats.ox.ac.uk/pub/yau/quantisnp2/download/b36.tar.gz
tar -zxvf b36.tar.gz
export GC_DIR=$INSTALL_DIR/b36

Installing HMMCopy

For this tutorial we will install HMMCopy. It is a Bioconductor package http://www.bioconductor.org/packages/release/bioc/html/HMMcopy.html.

We will start R.


and inside the R environment execute


where the last line was copied from the HMMcopy Bioconductor page. Follow along and accept any suggested updates.

HMMcopy also has C package associated with it. We will need to download this from http://compbio.bccrc.ca/software/hmmcopy.

wget http://compbio-bccrc.sites.olt.ubc.ca/files/2013/12/HMMcopy.zip
unzip http://compbio-bccrc.sites.olt.ubc.ca/files/2013/12/HMMcopy.zip
cd HMMcopy_0.1.1_14Dec2012

Installing TITAN

TITAN is available as a Bioconductor R package. We can install it in R. First open R:


In R, enter the following commands:

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