Getting Started

Open Terminal (OSX)

Click search icon in upper right-hand corner of desktop. Type "Terminal" and click on the application.

Clone the github repository to your local machine by typing:

cd /Temporary\ Files/
git clone https://github.com/shmohammadi86/RNASeq.git
sh

Type cd RNASeq so that you are working in the directory RNASeq, where all the working files are located.

Type ls to view the following subdirectories:

• datasets: Contains all the files for analysis

• tools: Contains all the analysis tools

• scripts: Contains all the scripts (code)

Set up paths so that tools can be run from within any directory

REPO="/Temporary Files/RNASeq"

for d in "$REPO"/tools/*; do 
   PATH="$PATH:$d"; 
done
export PATH

Following on your own laptop

If you are cloning the repository on your own computer, replace every occurrence of "Temporary\ Folder" with where you cloned the repository. Additionally, update the contents of tools/* folder with tools/archive/* with the related version of tools for your operating system.