Environment

#0-vi. Environment 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

You can place the RNA_HOME variable in your .bashrc and then logout and login again to avoid having to worry about it. This has been done for you in the pre-configured amazon instance that you will be using.

Additional environment varaibles used throughout this tutorial:

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

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