Advanced Linux Commands & Shell Scripting

A short presentation on Advanced Linux Commands & Shell Scripting delivered to aspiring bioinformaticians in Advanced Genomics & Bioinformatics Workshop held at ILRI, Nairobi.

Transcript

1. James Oguya Nairobi, Kenya August, 2016
2. $ man ls $ man cat • $ man man man less ◦ q man
3. ls ◦ cd ls ls ◦ $ ls ◦ $ ls -l
4. $ ls -a $ ls -la ls $ ls file99.txt $ ls ~ $ ls ~/earth
5. cp ◦ cp source destination • $ cp file1.txt file2.txt • $ mkdir files $ cp file2.txt files/ $ cp file1.txt file2.txt files/ $ cp -r files/ new-files/
6. mv ◦ mv source destination $ mv file1.txt file3.txt $ mv file3.txt new-files/ $ mv new-files/ old-files/ $ mv old-files/ files/ $ ls files/
7. ◦ rm file rm -r $ rm file2.txt $ rm -rf files/old-files
8. * ? ^ ◦ . .bashrc ◦ $ ls file* ◦ $ ls *.txt
9. ◦ ◦ ◦ $ echo “Current date and time is” > today.txt $ cat today.txt
10. $ date >> today.txt $ cat today.txt • $ cat < today.txt $ ls files/ file99.txt 2> stderr $ ls files/ file99.txt 1> output 2> error $ cat output $ cat error
11. $ ls files/ file99.txt &> streams $ cat streams
12. ◦ $ cat streams | wc -l $ ls -l | less $ cat streams | grep file | wc -l
13. ◦ ◦ wget URL $ wget http://hpc.ilri.cgiar.org/~joguya/gene-description.txt $ wget http://hpc.ilri.cgiar.org/~joguya/gene-description.txt -O gene-desc.txt
14. grep ◦ grep substring file • -i $ grep date today.txt $ grep protein_coding gene-description.txt | wc -l
15. ◦ head ◦ tail head tail ◦ commandA | head ◦ commandB | tail $ head -n5 gene-description.txt $ tail -n5 gene-description.txt
16. nano script1.sh echo "Date and time is:" date echo "Your current directory is:" pwd
17. script1.sh $ sh script1.sh • Date and time is: Mon Aug 8 12:30:54 EAT 2016 Your current directory is: /home/user1
18. nano script2.sh DATE=$(date) PWD=$(pwd) echo "Date and time is: $DATE" echo "Your current directory is: $PWD"
19. ◦ ◦ $(command) `command`
20. for arg in [list] do command(s)... done ◦ arg list
21. nano script3.sh for num in 1 2 3 do echo “we are on number: $num” done script3.sh $ sh script3.sh
22. script4.sh for num in {1..3} do echo “we are on number: $num” done script4.sh $ sh script4.sh
23. seq ◦ script5.sh for num in $(seq 1 3) do echo “we are on number: $num” done ◦ script5.sh $ sh script5.sh •