Wednesday, July 30, 2014

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 ( 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:
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

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

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