Environment Variables in Bioinformatics

Podcast

Play an AI-generated podcast conversation about this lesson

Download our mobile app to listen on the go

Get App

Questions and Answers

What do the numbers 666 and 644 represent in a file permission mode?

The file permission modes for users, groups, and others (correct)
The owner's user ID and group ID
The number of users and groups that can read and write a file
The type of file and its size

What is the main difference between the file permission modes 666 and 644?

The group's permissions are reversed
Others may write a file in 666 but not in 644 (correct)
The permissions are identical for both modes
The owner's permissions are reversed

What is a shell variable?

A type of environment variable
A command to print environment variables
A permanent storage location on a computer
An area of memory that can store information, referred to by a name (correct)

What is the purpose of the 'printenv' command?

To print the values of all environment variables (D) Signup and view all the answers

What is an environment variable?

A dynamic object that stores a value, referenced by one or more programs (B) Signup and view all the answers

What is one of the uses of environment variables?

To determine the directory to install files in (B) Signup and view all the answers

What is the difference between a shell variable and an environment variable?

Shell variables are used by the shell, while environment variables are used by programs (A) Signup and view all the answers

What is an advantage of using environment variables?

They can be referenced by one or more programs (C) Signup and view all the answers

What is the purpose of the HOME environment variable?

To show the current user's home directory (C) Signup and view all the answers

What does the PWD environment variable store?

The value of your current working directory (C) Signup and view all the answers

What is the purpose of the echo command?

To write arguments to the standard output (B) Signup and view all the answers

What is the purpose of using the `$` symbol with a variable in the echo command?

To print the value of the variable (A) Signup and view all the answers

What is the purpose of using backticks or the `$()` syntax in the echo command?

To ask the shell to substitute the results of a given command (D) Signup and view all the answers

What is a shell script?

A file containing a series of commands (C) Signup and view all the answers

What is the purpose of the PATH environment variable?

To contain a colon-separated list of directories that the system searches to find the executable program corresponding to a command (A) Signup and view all the answers

What is the purpose of using the `–e` option with the echo command?

To jump to another line (C) Signup and view all the answers

What is the purpose of the shebang line in a script?

To specify the interpreter to be used to execute the script (A) Signup and view all the answers

What is the effect of using `chmod u+x` on a script file?

It adds execute permissions to the owner of the file (B) Signup and view all the answers

What is the benefit of using variables in shell scripts?

It makes the script easier to maintain and reduces the amount of typing (A) Signup and view all the answers

What is the purpose of the `which` command in shell scripts?

To locate the executable file associated with a given command (C) Signup and view all the answers

What is the effect of using `chmod 744` on a script file?

It sets the file permission modes to read, write, and execute for the owner, and read-only for the group and others (A) Signup and view all the answers

What is an example of an absolute path to an interpreter in a script?

#!/usr/bin/perl (C) Signup and view all the answers

Flashcards are hidden until you start studying

Study Notes

Environment Variables

Environment variables help shape the environment where the commands are executed.
Examples of environment variables: HOME (current user's home directory), PATH (directories where the system searches for executable programs), PWD (current working directory).

Shell Scripting

Shell scripts are short programs written in a shell programming language to automate tasks under Linux OS.
A shell script is a file containing a series of commands.
Shell scripts are useful for performing the same actions on many different files.
Echo command is commonly used in shell scripts to display messages or instructions.

Echo Command

Syntax: echo options arguments
Writes arguments to the standard output.
Can be used to print results or ask the user for input.
Examples:
- echo "Bioinformatics is great \n starting writing scripts"
- echo –e “Bioinformatics is great \n starting writing scripts”
- X=firstvariable; echo X; echo $X

Running Commands and Substitution

Print the result of a command using backticks `` or $( ) parentheses.
Examples:
- echo pwd``
- echo $(pwd)

Shell Scripts

A shell script is a file containing a series of commands.
Shell script = scripting interpreter + command-line interface to the system.
Shell scripts can be used to automate tasks and display messages or instructions.

Creating a Shell Script

Steps to create a shell script:
1. Create a new file using a text editor (e.g., nano myfirstscript).
2. Write the script content (e.g., #!/bin/bash; echo "Hey, I am starting writing shell scripts").
3. Run the script using ./ (e.g., ./myfirstscript).
4. Change the file permissions to make it executable (e.g., chmod u+x myfirstscript or chmod 744 myfirstscript).

Shebang

#! is called the shebang, which indicates the beginning of a script.
The shebang is followed by the absolute path to an interpreter executable (e.g., /bin/bash or /usr/bin/perl).
The which command can be used to locate the executable file associated with a given command.