**This presentation originally developed by: Milad Fatenejad**
# What is the shell how do I access the shell?
**This presentation originally developed by: Milad Fatenejad**
# What is the shell how do I access the shell?
The shell is just a program and there are many different shell
programs that have been developed. The most common shell (and the one
we will use) is called the Bourne-Again SHell (bash). Even if bash is
The shell is just a program and there are many different shell
programs that have been developed. The most common shell (and the one
we will use) is called the Bourne-Again SHell (bash). Even if bash is
started by typing `bash` in the terminal. Many commands, especially a
lot of the basic ones, work across the various shells but many things
are different. I recommend sticking with bash and learning it well.
started by typing `bash` in the terminal. Many commands, especially a
lot of the basic ones, work across the various shells but many things
are different. I recommend sticking with bash and learning it well.
# The Example: Manipulating Experimental Data Files
We will spend most of our time learning about the basics of the shell
# The Example: Manipulating Experimental Data Files
We will spend most of our time learning about the basics of the shell
-One very basic command is `echo`. This command is just prints text to
-the terminal. Try entering the command:
+One very basic command is `echo`. This command just prints text to
+the terminal. Try the command:
Now, `cd` into the `Bert` directory and enter the command
`../smallest`. Notice that it says permission denied. This happens
because we haven't told the shell that this is an executable
Now, `cd` into the `Bert` directory and enter the command
`../smallest`. Notice that it says permission denied. This happens
because we haven't told the shell that this is an executable
-file. Enter the following commands:
+file. If you do `ls -l ../smallest`, it will show you the permissions on
+the left of the listing.
+
+Enter the following commands:
-You will see that the file name is green. Congratulations, you just
-created your first shell script!
+You will see that the file name is green and the permissions have changed.
+Congratulations, you just created your first shell script!