Environment setup

Directories and symlinks

Directories and links needed in your home directory.

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

.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.

cp .bashrc .bashrc.beforeNGS

Copy and configure the login profile for this class

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):

source ~/.bashrc

Start an idev session

To start an idev (interactive development) session:

idev -p normal -m 120 -N 1 -n 24 -A UT-2015-05-18 --reservation=CCBB

You can tell you're in a idev session because the hostname command will return a compute node name (e.g. nid00438) instead of a login node name (e.g. login5).

The n idev session will terminate when the requested time has expired, or you use the exit command.