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HPC Carpentry part 1 - Using the shell

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Scripts, variables, and loops

Overview

Teaching: 45 min
Exercises: 10 min
Questions

  • How do I turn a set of commands into a program?

Objectives

  • Write a shell script

  • Understand shell variables and how to use them

  • Write a simple for loop

  • Understand and manipulate UNIX permissions

We now know a lot of UNIX commands! Wouldn’t it be great if we could save certain commands so that we could run them later or not have to type them out again? As it turns out, this is straightforward to do. A “shell script” is essentially a text file containing a list of UNIX commands to be executed in a sequential manner. These shell scripts can be run whenever we want, and are a great way to automate our work.

Writing a Script

So how do we write a shell script, exactly? It turns out we can do this with a text editor. Start editing a file called “demo.sh” (to recap, we can do this with nano demo.sh). The “.sh” is the standard file extension for shell scripts that most people use (you may also see “.bash” used).

Our shell script will have two parts:

Our file should now look like this:

#!/bin/bash

echo "Our script worked!"

Ready to run our program? Let’s try running it:

$ bash demo.sh

Fantastic, we’ve written our first program! Before we go any further, let’s learn how to take notes inside our program using comments. A comment is indicated by the # character, followed by whatever we want. Comments do not get run. Let’s try out some comments in the console, then add one to our script!

# This wont show anything

Now lets try adding this to our script with nano. Edit your script to look something like this:

#!/bin/bash

# This is a comment... they are nice for making notes!
echo "Our script worked!"

When we run our script, the output should be unchanged from before!

Shell variables

One important concept that we’ll need to cover are shell variables. Variables are a great way of saving information under a name you can access later. In programming languages like Python and R, variables can store pretty much anything you can think of. In the shell, they usually just store text. The best way to understand how they work is to see them in action.

To set a variable, simply type in a name containing only letters, numbers, and underscores, followed by an = and whatever you want to put in the variable. Shell variable names are often uppercase by convention (but do not have to be).

$ VAR="This is our variable"

To use a variable, prefix its name with a $ sign. Note that if we want to simply check what a variable is, we should use echo (or else the shell will try to run the contents of a variable).

$ echo $VAR

This is our variable

Let’s try setting a variable in our script and then recalling its value as part of a command. We’re going to make it so our script runs wc -l on whichever file we specify with FILE.

Our script:

#!/bin/bash

# set our variable to the name of our GTF file
FILE=dmel-all-r6.19.gtf

# call wc -l on our file
wc -l $FILE

$ bash demo.sh

542048 dmel-all-r6.19.gtf

What if we wanted to do our little wc -l script on other files without having to change $FILE every time we want to use it? There is actually a special shell variable we can use in scripts that allows us to use arguments in our scripts (arguments are extra information that we can pass to our script, like the -l in wc -l).

To use the first argument to a script, use $1 (the second argument is $2, and so on). Let’s change our script to run wc -l on $1 instead of $FILE. Note that we can also pass all of the arguments using $@ (not going to use it in this lesson, but it’s something to be aware of).

Our script:

#!/bin/bash

# call wc -l on our first argument
wc -l $1

$ bash demo.sh dmel_unique_protein_isoforms_fb_2016_01.tsv

22129 dmel_unique_protein_isoforms_fb_2016_01.tsv

Nice!

Capturing the output of commands

One thing to be aware of when using variables: they are all treated as pure text. How do we save the output of an actual command like ls?

A demonstration of what doesn’t work:

$ TEST=ls
$ echo $TEST

ls

What does work (we need to surround any command with $(command)):

$ TEST=$(ls -l)
$ echo $TEST

total 90372 -rw-rw-r--. 1 jeff jeff 12534006 Jan 16 18:50 bash-lesson.tar.gz -rwxrwxr-x. 1 jeff jeff 40 Jan 1619:41 demo.sh -rw-rw-r--. 1 jeff jeff 77426528 Jan 16 18:50 dmel-all-r6.19.gtf -rw-r--r--. 1 jeff jeff 721242 Jan 25 2016 dmel_unique_protein_isoforms_fb_2016_01.tsv drwxrwxr-x. 2 jeff jeff 4096 Jan 16 19:16 fastq -rw-r--r--. 1 jeff jeff 1830516 Jan 25 2016 gene_association.fb.gz -rw-rw-r--. 1 jeff jeff 15 Jan 16 19:17 test.txt -rw-rw-r--. 1 jeff jeff 245 Jan 16 19:24 word_counts.txt

Note that everything got printed on the same line. This is a feature, not a bug, as it allows us to use $(commands) inside lines of script without triggering line breaks (which would end our line of code and execute it prematurely).

Loops

To end our lesson on scripts, we are going to learn how to write a for-loop to execute a lot of commands at once. This will let us do the same string of commands on every file in a directory (or other stuff of that nature).

for-loops generally have the following syntax:

#!/bin/bash

for VAR in first second third
do
    echo $VAR
done

When a for-loop gets run, the loop will run once for everything following the word in. In each iteration, the variable $VAR is set to a particular value for that iteration. In this case it will be set to first during the first iteration, second on the second, and so on. During each iteration, the code between do and done is performed.

Let’s run the script we just wrote (I saved mine as loop.sh).

$ bash loop.sh

first
second
third

What if we wanted to loop over a shell variable, such as every file in the current directory? Shell variables work perfectly in for-loops. In this example, we’ll save the result of ls and loop over each file:

#!/bin/bash

FILES=$(ls)
for VAR in $FILES
do
        echo $VAR
done

$ bash loop.sh

bash-lesson.tar.gz
demo.sh
dmel_unique_protein_isoforms_fb_2016_01.tsv
dmel-all-r6.19.gtf
fastq
gene_association.fb.gz
loop.sh
test.txt
word_counts.txt

There’s actually even a shortcut to run on all files of a particular type, say all .gz files:

#!/bin/bash

for VAR in *.gz
do
    echo $VAR
done

bash-lesson.tar.gz
gene_association.fb.gz

Writing our own scripts and loops

cd to our fastq directory from earlier and write a loop to print off the name and top 4 lines of every fastq file in that directory.

Is there a way to only run the loop on fastq files ending in _1.fastq?

Solution

Create the following script in a file called head_all.sh

#!/bin/bash

for FILE in *.fastq
do
   echo $FILE
   head -n 4 $FILE
done

The “for” line could be modified to be for FILE in *_1.fastq to achieve the second aim

Concatenating variables

Concatenating (i.e. mashing together) variables is quite easy to do. Add whatever you want to concatenate to the beginning or end of the shell variable after enclosing it in {} characters.

FILE=stuff.txt
echo ${FILE}.example

stuff.txt.example

Can you write a script that prints off the name of every file in a directory with “.processed” added to it?

Solution

Create the following script in a file called process.sh

#!/bin/bash

for FILE in *
do
   echo ${FILE}.processed
done

Note that this will also print directories appended with “.processed”. To truely only get files and not directories, we need to modify this to use the find command to give us only files in the current directory:

#!/bin/bash

for FILE in $(find . -max-depth 1 -type f)
do
   echo ${FILE}.processed
done

but this will have the side-effect of listing hidden files too.

Running a script like a linux command

We can save a little typing time by running our script like any other Linux command (eg ls) instead of having to type ‘bash’ before each command. This takes a bit of set up.

If we type:

$ demo.sh

bash: demo.sh: command not found...

Bash can’t find our script. As it turns out, Bash will only look in certain directories for scripts to run. To run anything else, we need to tell Bash exactly where to look. To run a script that we wrote ourselves, we need to specify the full path to the file, followed by the filename. We could do this one of two ways: either with our absolute path /lustre/home/tc008/yourUserName/demo.sh, or with the relative path ./demo.sh.

$ ./demo.sh

bash: ./demo.sh: Permission denied

There’s one last thing we need to do. Before a file can be run, it needs “permission” to run. Let’s look at our file’s permissions with ls -l:

$ ls -l

-rw-rw-r--. 1 yourUsername tc001 12534006 Jan 16 18:50 bash-lesson.tar.gz
-rw-rw-r--. 1 yourUsername tc001       40 Jan 16 19:41 demo.sh
-rw-rw-r--. 1 yourUsername tc001 77426528 Jan 16 18:50 dmel-all-r6.19.gtf
-rw-r--r--. 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_isoforms_fb_2016_01.tsv
drwxrwxr-x. 2 yourUsername tc001     4096 Jan 16 19:16 fastq
-rw-r--r--. 1 yourUsername tc001  1830516 Jan 25  2016 gene_association.fb.gz
-rw-rw-r--. 1 yourUsername tc001       15 Jan 16 19:17 test.txt
-rw-rw-r--. 1 yourUsername tc001      245 Jan 16 19:24 word_counts.txt

That’s a huge amount of output. Let’s see if we can understand what it is, working left to right.

So how do we change permissions? As I mentioned earlier, we need permission to execute our script. Changing permissions is done with chmod. To add executable permissions for all users we could use this:

$ chmod +x demo.sh
$ ls -l

-rw-rw-r--. 1 yourUsername tc001 12534006 Jan 16 18:50 bash-lesson.tar.gz
-rwxrwxr-x. 1 yourUsername tc001       40 Jan 16 19:41 demo.sh
-rw-rw-r--. 1 yourUsername tc001 77426528 Jan 16 18:50 dmel-all-r6.19.gtf
-rw-r--r--. 1 yourUsername tc001   721242 Jan 25  2016 dmel_unique_protein_isoforms_fb_2016_01.tsv
drwxrwxr-x. 2 yourUsername tc001     4096 Jan 16 19:16 fastq
-rw-r--r--. 1 yourUsername tc001  1830516 Jan 25  2016 gene_association.fb.gz
-rw-rw-r--. 1 yourUsername tc001       15 Jan 16 19:17 test.txt
-rw-rw-r--. 1 yourUsername tc001      245 Jan 16 19:24 word_counts.txt

Now that we have executable permissions for that file, we can run it.

$ ./demo.sh

Our script worked!

Special permissions

What if we want to give different sets of users different permissions. chmod actually accepts special numeric codes instead of stuff like chmod +x. The numeric codes are as follows: read = 4, write = 2, execute = 1. For each user we will assign permissions based on the sum of these permissions (must be between 7 and 0).

Let’s make an example file and give everyone permission to do everything with it.

touch example
ls -l example
chmod 777 example
ls -l example

How might we give ourselves permission to do everything with a file, but allow no one else to do anything with it.

Solution

chmod 700 example

We want all permissions so: 4 (read) + 2 (write) + 1 (execute) = 7 for user (first position), no permissions, i.e. 0, for group (second position) and all (third position).

Key Points

  • A shell script is just a list of bash commands in a text file.

  • You can use variables and loops to automate tasks that were previously done by hand

  • chmod +x script.sh will give a script permission to execute.

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