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. 

Because I did such a horrid job taking comprehensible notes while in London, I am going to be more efficient this time around with transcriptome assembly.

We have our illumina RNA-seq reads back (yay!).

To download the reads from UArizona, you have to download this horridly complicated program called irods (http://uagc.arl.arizona.edu/resources/user-guide). After much struggle, the easiest way to get things installed and compiled is the "non-fancy" way. HOWEVER, you MUST download the most recent version of iRods (as of right now 3.3.1)

Navigate to your iRODs folder. Things in blue are what you type. Things in pink are what you would change differently based on your computer.

 export PATH=$PATH:$HOME/iRODS/clients/icommands/bin

 iinit #this will prompt you for a bunch of information

Enter the host name (DNS) of the server to connect to:  mozart.arl.arizona.edu

Enter the port number:  1247

Enter your irods user name:  <your login name from UAGC/BCF>

Enter your irods zone:  BCFZone

Enter your current iRODS password:  <your password from UAGC/BCF>

 

#now your session should start

ils #lists all of the folders in your iRODS account

icd 14140709_SN885_0197_Lane1SideA_Project_Davalos_RNA #change directory

iget -r 140709_SN885_0197_Lane1SideA_Project_Davalos_RNA /Volumes/Spare/ 

#iget -r copies the folder you want to whatever directory you want

Okay now all of the data should be on your computer.

Now I need to install Trinity:

#install homebrew if you do not already have it

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

#now install programs necessary for trinity to run on your mac

brew install homebrew/science/bowtie

brew install git

#to allow for new installation of compiler

brew tap homebrew/dupes

brew install apple-gcc42

#okay guess I can't do that because it requires an operating system higher than Mac OSX Lion...

Yes, you read that correctly. Our operating system is still pre-lion. Seems like I will have to wait until our operating system is figured out.

Once we figure this out though, remember this link: http://sourceforge.net/p/trinityrnaseq/mailman/message/31892980/

It allows for trinity to be installed on Mac (even though it is compiled for Linux).