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# 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

Copying files between TACC and your laptop

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Copying files to/from TACC Copying files to/from

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TACC

Assume you want to copy the TACC file $SCRATCH/core_ngs/fastq_prep/small_fastqc.html back to your laptop/local computer. You must initiate the copy operation from your local computer rather than at TACC. Why? because the TACC servers have host names and IP addresses that are public in the Internet's Distributed Name Service (DNS) directory. But your local computer (in nearly all cases) does not have a published name and address.

First, on the TACC server figure out what the appropriate absolute path (a.k.a. full pathname) is on TACC.

cd $SCRATCH/core_ngs/fastq/prep
pwd -P

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