Part 6 Appendices

6.1 Other workshop files

6.2 Local access of files on the HPC

Mac: 1. Click Finder > “Go” in task bar > “Connect to Server” in the pulldown menu. 2. Type smb://pn.vai.org and click “Connect”. 3. Select ‘projects’ and ‘researchtemp’. Click “OK”. 4. You can now navigate using Finder, or type ls /Volumes/projects/ or ls /Volumes/researchtemp/ in the Terminal.

Windows: * In File Explorer, type \\pn.vai.org\ and hit Enter.

6.3 Bash cheatsheet

Name	Command Line	Description	Example
Print Working Directory	`pwd`	Displays the current working directory	`[username\@submit002 ~]$ pwd` Result:/home/username
List	`ls`	Lists the files and directories in the current directory	`[username\@submit002 ~]$ ls` Result: It returns empty after the $ symbol since nothing has been created.
List More Detail	`ls -lht`	Display more details about the file	`[username\@submit002 ~]$ ls -lht` Result: Display file detail in the current director
Make Directory	`mkdir`	Creates a new directory	`[username\@submit002 ~]$ mkdir hpc_mini_workshop` Result: A hpc_mini_workshop folder is created.
Move	`mv`	Moves or renames files or directories	`[username\@submit002 ~]$ mv hpc_mini_workshop workshopTraining` Result: Now the hpc_mini_workshop directory is called workshopTraining
Change Directory	`cd`	Change to an existing directory	`[username\@submit002 ~]$ cd workshopTraining` Result: [username@submit002 workshopTraining]$ Notice ~ was in the home directory, now in the workshopTraining directory.
Remove	`rm`	Deletes files and directories	`[username\@submit002 ~]$ rm -r TaskProject` *Note: -r means directory Result: TaskProject is deleted
Copy	`cp`	Copies files or directories	`[username\@submit002 ~]$ cp -r Task1 Project` Result: Task1 directory has moved to the Project directory.
Search for File	`find`	Search for files and directories based on various criteria like name, size, and modification time	`[username\@submit002 ~]$ find Project` Result: Task1 will appear within the Project directory Project Project/Task1
Head	`head`	Display at the beginning of a file	`[username\@submit002 ~]$ head -n5 file_name` Result: It will display the first 5 lines from the beginning of the file_name.
Tail	`tail`	Display at the end of a file	`[username\@submit002 ~]$ tail -n5 file_name` Result: It will display the last 5 lines from the end of the file_name
Less	`less`	Load the necessary portion of a file	`[username\@submit002 ~]$ less file.txt` Result: The user is able to view a portion of the file.txt.
More	`more`	Load the entire file	`[username\@submit002 ~]$ more file.txt` Result: The user is able to view the entire file.txt.
Quit	`q`	Stop viewing the current file	quit viewing the current file
Concatenate	`cat`	Display the contents of a file	`[username\@submit002 ~]$ cat file.txt` Result: Display the contents of file.txt
Search for Text	`grep`	Search for a specific pattern of text within files	`[username\@submit002 ~]$ grep “GCGGA” sequence_file.fastq` Result: Display any GCGGA pattern in sequence_file.fastq
Word, Line, and Character Count	`wc`	Display the number of words, lines, and characters in a file	`[username\@submit002 ~]$ wc file.txt` Result: Display the number of words, lines, and characters in the file.txt.
Touch	`touch`	Create a new empty file	`[username\@submit002 ~]$ touch exampleFile.txt` Result: The command line will display file details in the current directory