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Normally you should not perform significant computation on login nodes, since they are shared by all users in the TACC community. Well, there are a  few exceptions, and login5.ls5.tacc.utexas.edu is one of them. Is it a dedicated login node owned by CSSB and CBRS, so we have given you access to it for the duration of this course. This will let us do a few things at the command line that would normally set off alarm bells from the TACC folks if we all did them on a standard login node.

Data staging

Recall that yesterday we copied some FASTQ data to our "permanent archive area".

Get the yeast data if you haven't already.

mkdir -p $WORK/archive/original/2018_05.core_ngs
cd $WORK/archive/original/2018_05.core_ngs
wget http://web.corral.tacc.utexas.edu/BioinformaticsResource/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
wget http://web.corral.tacc.utexas.edu/BioinformaticsResource/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

mkdir -p $WORK/archive/original/2018_05.core_ngs
cd $WORK/archive/original/2018_05.core_ngs
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/yeast_stuff/Sample_Yeast_L005_R[12].cat.fastq.gz .

Set ourselves up to process some yeast data data in $SCRATCH, using some of best practices for organizing our workflow.

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