OSX installation

To set up your own computer for today’s session, follow these instructions. Copying and pasting the given code may be the easiest way to make sure everything works.

Open a Terminal Applications -> Utilities -> Terminal.
If you don’t have homebrew installed, type the following to your terminal. If you do have homebrew installed, please skip to the next step

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

If you haven’t installed the commands sed and wget in the Bash workshop last week, then install them now:

brew install gnu-sed --default-names
brew install wget
echo "export PATH=\${PATH}:/usr/local/Cellar/gnu-sed/4.4/bin:/usr/local/Cellar/wget/1.19.1_1/bin" >> ~/.bash_profile

Install NGS tools: fastqc, cutadapt, bwa, samtools, bcftools, freebayes, sabre, IGV, picard

brew update
brew upgrade
brew tap homebrew/science
brew install fastqc
brew install cutadapt
brew install bwa
brew install samtools
brew install bcftools
brew install freebayes
brew install picard-tools

Install sabre

brew install git
git clone https://github.com/najoshi/sabre
cd sabre
make
SABRE_HOME=`pwd`
echo "export PATH=\${PATH}:${SABRE_HOME}" >> ~/.bash_profile

Download IGV

wget http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.0.app.zip

After completing the above steps, close the terminal then open it again to start.

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