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Table of Contents

Environment setup

Directories and links needed in your home directory.

Code Block
languagebash
cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK work
ln -s -f /work/projects/BioITeam

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /work/projects/BioITeam/common/bin/launcher_maker.py
ln -s -f /work/projects/BioITeam/ls5/opt/cutadapt-1.10/bin/cutadapt
ln -s -f /work/projects/BioITeam/ls5/opt/multiqc-1.0/multiqc
ln -s -f /work/projects/BioITeam/ls5/opt/samstat-1.09/samstat

Anchor
Catchup_bashrc
Catchup_bashrc
.bashrc setup

If you already have a .bashrc set up, make a backup copy first. You can restore your original login script after class is over.

Code Block
languagebash
cd
cp .bashrc .bashrc.beforeNGS

Copy and configure the login profile for this class

Code Block
languagebash
titleCopy a pre-configured login script
cd
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5  .bashrc
chmod 600 .bashrc

Source it to make it active (if this doesn't work, log off then log back in):

Code Block
languagebash
titleCopy a pre-configured login script
source ~/.bashrc

Anchor
Catchup_idev
Catchup_idev
Start an idev session

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