Environment
Getting Started
This tutorial assumes use of a Linux computer with an ‘x86_64’ architecture. The rest of the tutorial should be conducted in a linux Terminal session. In other words you must already be logged into the Amazon EC2 instance as described in the previous section.
Before proceeding you must define a global working directory by setting the environment variable: ‘RNA_HOME’ Log into a server and SET THIS BEFORE RUNNING EVERYTHING.
Create a working directory and set the ‘RNA_HOME’ environment variable
mkdir -p ~/workspace/rnaseq/
export RNA_HOME=~/workspace/rnaseq
Make sure whatever the working dir is, that it is set and is valid
echo $RNA_HOME
Since all the environment variables we set up for the RNA-seq workshop start with ‘RNA’ we can easily view them all by combined use of the env and grep commands as shown below. The env command shows all environment variables currently defined and the grep command identifies string matches.
env | grep RNA
You can place the RNA_HOME variable (and other environment variables) in your .bashrc and then logout and login again to avoid having to worry about it. A .bashrc file with these variables has already been created for you.
In order to view the contents of this file, you can type:
less ~/.bashrc
To exit the file, type q.
Environment variables used throughout this tutorial:
export RNA_HOME=~/workspace/rnaseq
export RNA_DATA_DIR=$RNA_HOME/data
export RNA_DATA_TRIM_DIR=$RNA_DATA_DIR/trimmed
export RNA_REFS_DIR=$RNA_HOME/refs
export RNA_REF_INDEX=$RNA_REFS_DIR/chr22_with_ERCC92
export RNA_REF_FASTA=$RNA_REF_INDEX.fa
export RNA_REF_GTF=$RNA_REF_INDEX.gtf
export RNA_ALIGN_DIR=$RNA_HOME/alignments/hisat2
We will be using picard tools throughout this workshop. To follow along, you will need to set an environment variable pointing to your picard installation.
export PICARD=/home/ubuntu/bin/picard.jar
For simplicity, we are going to download a preconfigured .bashrc file to use.
cd ~
wget http://genomedata.org/rnaseq-tutorial/bashrc_copy
mv bashrc_copy ~/.bashrc
source ~/.bashrc
Now if you run the following command, you should see the RNA environment variables present.
env | grep RNA
Alternatively, you could have add these enivroment variables manually if they were not part of your .bashrc. First, you can open your .bashrc file with nano by simply typing:
nano ~/.bashrc
You can now see the contents of this file. Then, you want to add the above environment variables to the bottom of the file. You can do this by copying and pasting. Once you have the variables in the file, you’ll want to type ctrl + o to save the file, then enter to confirm you want the same filename, then ctrl + x to exit nano.
Again, check all the RNA related environment variables to make sure things look right.
env | grep RNA
Note that if you are doing this course on the Google Cloud Platform instead of AWS, you should instead use this .bashrc file: http://genomedata.org/rnaseq-tutorial/bashrc_copy_gcp.sh