Useful command line shortcuts¶

Command	Function	Example
`cat`	Read and print contents of a file	`cat my_file.txt`
`grep`	Search a file for lines containing text of interest	`grep "words" my_file.txt`
`sed`	Find and replace text in a file	`sed 's/words/pictures/' my_file.txt`
`head`	Print the first n lines from a file	`head -n 10 my_file.txt`
`tail`	Print the last n lines from a file	`tail -n 10 my_file.tx`t
`less`	Partially open a text file for viewing, reading lines as the user scrolls	`less my_file.txt`
`cut`	Retrieve particular columns of a file. Uses tab as the delimiting character, can change with `-d` parameter	`cut -f1,2,5 -d "," my_file.txt`
`paste`	Opposite of `cut`, stitch together files in a row-wise manner	`paste my_file.txt my_other_file.txt`

Command	Function
`Ctrl` + `X`	Close the file
`Ctrl` + `O`	Save the file
`Ctrl` + `W`	Search for a string in the file
`Ctrl` + `Space`	Go forward one word in a line
`Alt` + `Space`	Go backwards one word in a line
`Ctrl` + `A`	Go to the beginning of a line
`Ctrl` + `E`	Go to the end of a line
`Ctrl` + `W`, `Ctrl` + `V`	Go to the last line of the file
`Ctrl` + `K`	Cut the current line and save it to the clipboard
`Ctrl` + `U`	Paste (Un-cut) the text in the clipboard
`Ctrl` + `Shift` + `6`	Select text

Command	Function	Example
`sbatch`	Submits a SLURM script to the queue manager	`sbatch job.sl`
`squeue`	Display jobs in the queue Display jobs belonging to user usr9999 Display jobs on the long partition	`squeue` `squeue -u usr9999` `squeue -p long`
`sacct`	Displays all the jobs run by you that day Display job 123456789	`sacct` `sacct -j 123456789`
`scancel`	Cancel a queued or running job Cancel all jobs belonging to usr9999	`scancel 123456789` `scancel -u usr9999`
`sshare`	Shows the Fair Share scores for all projects of which usr9999 is a member	`sshare -U usr9999`
`sinfo`	Shows the current state of the SLURM partitions	`sinfo`
`sview`	Launches a GUI for monitoring SLURM jobs	`sview`

Most of these commands have a single character shortcut that you can use instead. These can be found by running

man sbatch

While logged into NeSI.

Command	Description	Example
`--job-name`	The name that will appear when using `squeue` or `sacct`	`#SBATCH --job-name=MyJob`
`--account`	The account to which your core hours will be 'charged'	`#SBATCH --account=nesi9999`
`--time`	Job max walltime. After this duration, the job will be terminated	`#SBATCH --time=DD-HH:MM:SS`
`--mem`	Memory required by the job. If exceeded the job will be termintated	`#SBATCH --mem=30GB`
`--cpu`	Number of CPUs to use for multithreading	`#SBATCH --cpu=20`
`--partition`	NeSI partition for job to run (default is large)	`#SBATCH --partition=long`
`--output`	Path and name of standard output file	`#SBATCH --output=output.out`
`--error`	Path and name of standard error file	`#SBATCH --output=output.err`
`--mail-user`	Address to send mail notifications	`#SBATCH --mail-user=bob123@gmail.com`
`--mail-type`	When to send mail notifications Will send a mail notification at BEGIN/END/FAIL Will send message at 80% walltime	`#SBATCH --mail-type=ALL` `#SBATCH --mail-type=TIME_LIMIT_80`
`--ntasks`	Number of MPI tasks to use It is very rare to use this option in bioinformatics