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How to set up a developer workstation

This guide assumes you are working on a system where you do not have administrator privelages. If you want to install software for all users, change the prefix argument to configure/make accordingly.

Basic settings

Copy the file "settings_template.R" to "settings.R" and change the values according to your environment. You won't know the values for some of the variables until after completing all the installation steps below.

Setting up exomeCNV

  1. Install R.

     wget http://cran.stat.sfu.ca/src/base/R-3/R-3.1.1.tar.gz
 tar xf R-3.1.1.tar.gz
 cd R-3.1.1
 ./configure --prefix=$HOME && make && make install

  2. Install samtools (requires ncurses development libraries).

     wget -O samtools-1.0.tar.bz2 http://sourceforge.net/projects/samtools/files/latest/download?source=files 
 tar xf samtools-1.0.tar.bz2
 cd samtools-1.0
 make && make prefix=$HOME install

  3. Register for an account with the Broad Institute (in order to download GATK). Go to this website.

     https://www.broadinstitute.org/gatk/download

    It will prompt you to log in or register. Click "register", follow the prompts, and wait for a confirmation email.

  4. Install GATK. Once you have an account, go back to the download page, click "GATK" (you don't need Queue). Navigate to where the archive is, then do

     tar xf GenomeAnalysisTK-3.2-2.tar.bz2

    This will produce a jar file. To use GATK more easily, copy the jar file to $HOME/bin, then create an executable script called "gatk" in $HOME/bin with the following contents.

     #!/bin/sh
 java -jar $HOME/bin/GenomeAnalysis.jar "$@"

  5. Install the DNAcopy R package. From the R console:

     source("http://bioconductor.org/biocLite.R")
 biocLite("DNAcopy")

  6. Install ExomeCNV. First get the file.

     wget http://cran.r-project.org/src/contrib/Archive/ExomeCNV/ExomeCNV_1.4.tar.gz

    Then from the R console:

     install.packages("ExomeCNV_1.4.tar.gz", repos=NULL, type="source")

Setting up HMMcopy

You should already have R installed from the previous step.

  1. Install HMMcopy.

     wget http://compbio.bccrc.ca/files/2013/12/HMMcopy.zip
 unzip HMMcopy.zip
 rm -rf __MACOSX
 cd HMMcopy
 cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME .
 make

  2. Copy the binaries to $HOME/bin.

     mkdir -p $HOME/bin
 cp bin/* $HOME/bin

  3. Add the following line to your ~/.bash_profile.

     export PATH=$PATH:$HOME/bin

  4. Install the HMMcopy R package. In the R console:

     source("http://bioconductor.org/biocLite.R")
 biocLite("HMMcopy")

Setting up Lumpy

  1. Install yaha.

     wget http://faculty.virginia.edu/irahall/support/yaha/YAHA.0.1.82.tar.gz
 tar xf YAHA.0.1.82.tar.gz
 mv yaha $HOME/bin

  2. Install Lumpy.

     wget -O lumpy-sv-0.2.7.tar.gz https://github.com/arq5x/lumpy-sv/releases/download/0.2.7/lumpy-sv-0.2.7.tar.gz
 tar xf lumpy-sv-0.2.7.tar.gz
 cd lumpy-sv-0.2.7
 make
 cp scripts/* $HOME/bin

Setting up TITAN

  1. Install the TitanCNA R package. From R:

     source("http://bioconductor.org/biocLite.R")
 biocLite("BiocUpgrade")
 biocLite("TitanCNA")

    Note that you must be running BioConductor >= 2.14, which is only available for R 3.1. The instructons on the TITAN website state that you need R 3.0.2, but this is incorrect.

  2. Install bcftools.

     wget -O bcftools-1.1.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2/download
 tar xf bcftools-1.1.tar.bz2
 cd bcftools-1.1
 make
 cp bcftools $HOME/bin

  3. Download TITANRunner.

     wget http://compbio.bccrc.ca/files/2013/07/TITANRunner-0.1.1.zip
 unzip TITANRunner-0.1.1.zip
 cd TITANRunner

  4. Obtain a local copy of dbSNP in VCF format.

     wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b141_GRCh37p13/VCF/common_all.vcf.gz

  5. Copy config_default.cfg to config.cfg and change the values to suit your environment.

  6. Follow the installation instructions (here)[http://compbio.bccrc.ca/software/titan/titan-installation/].

Other tools

  1. Download Picard tools.

     wget -O picard-tools-1.119.zip http://sourceforge.net/projects/picard/files/latest/download?source=files
 unzip picard-tools-1.119.zip
 cd picard-tools-1.119
 cp * $HOME/bin