Environment setup
Directories and symlinks
Directories and links needed in your home directory.
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
.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.
cd cp .bashrc .bashrc.beforeNGS
Copy and configure the login profile for this class
Copy 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):
Copy a pre-configured login script
source ~/.bashrc
Start an idev session
To start an idev (interactive development) session:
Start an idev 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.