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Code Block
languagebash
cd 
ln -s -f $SCRATCH scratch
ln -s -f $WORK$WORK2 workwork2
ln -s -f /workwork2/projects/BioITeam

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /workwork2/projects/BioITeam/commonprojects/bincourses/launcher_maker.py
ln -s -f /work/projects/BioITeam/ls5/opt/cutadapt-1.10/bin/cutadaptCore_NGS_Tools CoreNGS

mkdir -p ~/local/bin
cd ~/local/bin
ln -s -f /workwork2/projects/BioITeam/ls5common/opt/multiqc-1.0/multiqcbin/launcher_creator.py
ln -s -f /workwork2/projects/BioITeam/ls5common/opt/samstat-1.09/samstatbin/launcher_maker.py

Anchor
Catchup_bashrc
Catchup_bashrc
.bashrc setup

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Code Block
languagebash
cd
cp .bashrc .bashrc.beforeNGSbeforeNGSTools

Copy and configure the login profile for this class

Code Block
languagebash
cd
cp /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5stampede2  .bashrc
chmod 600 .bashrc

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