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Welcome to the EPP622 Test2!

EPP622 Test 2

Your Name: Alexandra Duckworth

Server: /lustre/isaac24/proj/UTK0505/aduckwo4/622_test2

Repository URL: https://github.com/aduckwo4-boop/EPP622-2026-SNPCalling/wiki

Setup

Create directory and symbolically linked provided files including the reference genome, reads, and the ground truth.

cd /lustre/isaac24/proj/UTK0505/aduckwo4
mkdir 622_test2
cd 622_test2
nano link_data.sh
#cd: changes to directory
#mkdir: creates new directory

Made link_data.sh

for file in /lustre/isaac24/proj/UTK0505/test2/ref
do
  	echo $file
    ln -s $file .
done

# for: loops through the specified file or directory path.
# echo: prints the file path to the terminal.
# ln -s: creates a symbolic link to the reference genome directory.
# .: places the symbolic link in the current directory.
# done: ends the for loop.

Created link_reads.sh

nano link_reads.sh

for file in /lustre/isaac24/proj/UTK0505/test2/reads
do
	echo $file
	ln -s $file .
done

#same as above

Created link.check.sh

nano link_check.sh

for file in /lustre/isaac24/proj/UTK0505/test2/check
do
  echo $file
  ln -s $file .
done
#same as above

Ran all three

bash link_data.sh
bash link_reads.sh
bash link_check.sh
# bash: executes each shell script.
# link_data.sh: links the reference genome directory.
# link_reads.sh: links the sequencing reads directory.
# link_check.sh: links the evaluation files directory.