| Show your current path |
pwd |
| List the contents of a folder |
ls, eg. ls or ls /home |
| Change directory |
cd directory, e.g. cd /home/ |
| Move/rename a file |
mv from to, e.g. mv data/genome.dat genomes/S001_genome.dat |
| Remove a file |
rm file or rm -rf dir/; use -i for confirmation |
| Make an empty file |
touch, e.g. touch commands.sh |
| Edit a file |
nano file, e.g. nano commands.sh |
| Show contents of a file |
cat file or less file, e.g. cat commands.sh |
| History of commands |
history, or the arrow keys |
| Command help |
man command, or command --help, or command -h |
| Connect to remote computer |
ssh username@hostname, e.g. ssh jp@scc.camh.net |
| Number of lines in a file |
wc -l file |
| Sort lines in a file |
sort file, or numerically sort -n file |
| Find lines in a file |
grep pattern file, e.g. grep M demographics.csv |
| Connect commands together |
command1 | command2, e.g. grep M file | sort |
| Save output to a file |
command > file, e.g. sort file > sorted-file.txt |
| Loop through a list |
for var in list; do stuff; done e.g. for i in 1 2 3; do echo ${i}; done |
| Find the last part of a path |
basename path, e.g. basename data/S013 |