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idev -p developmentnormal -m 60 -A UT-2015-05-18 -N 1 -n 68 --reservation=BIO_DATA_week_1

# Create a $SCRATCH area to work on data for this course,
# with a sub-direct[1orydirectory for pre-processing raw fastq files
mkdir -p $SCRATCH/core_ngs/fastq_prep

# Make a symbolic links to the original yeast data:
cd $SCRATCH/core_ngs/fastq_prep
ln -s -f $CORENGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f $CORENGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz
# or
ln -s -f ~/CoreNGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f /work~/CoreNGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

# or
ln -s -f /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

The bash shell lets you put multiple commands on one line if they are each separated by a semicolon ( ; ). So in the above for loop, you can see that bash consideres considers the do keyword to start a separate command. Two alternate ways of writing the loop are:

# One line for each clause, no semicolons
for <variable name> in <expression>
do 
  <something>
  <something else>
done

# All on one line, with semicolons separating clauses
for <variable name> in <expression>; do <something>; <something else>; done