Okay we have FINALLY updated our operating system.

Apparently Mavericks already has commandline tools installed so it is not necessary to install again. However, there are some issues if you install Homebrew and the gcc compiler not being linked. So starting from scratch, here is what do do.

#install homebrew

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

#check to see your comp is ready to brew

brew doctor

#i had several errors/warnings (errors indicated in orange)

/usr/bin comes before /usr/local/bin

export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

/usr/local/lib/gcc is not writable.

sudo chown -R laurelyohe /usr/local

brew install homebrew/science/bowtie

brew install apple-gcc42

brew install samtools

brew install trinity

Okay, everything seems good to go. Now I am unzipping the transcriptome output from trimmomatic.