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Software Exercise 2.1 Build an HTC-Friendly Executable

Objective: Modify an existing script to include arguments and headers.

Why learn this?: A little bit of preparation can make it easier to reuse the same script over and over to run many jobs.


  1. Download and unzip a set of Protein Data Bank (PDB) files:

    $ wget
    $ tar -xzf alkanes.tar.gz
  2. For these exercises, we are going to run a command that counts the number of atoms in the PDB file . Run it now as an example:

    $ grep ATOM cubane.pdb | wc -l > atoms_cubane.pdb

Add a Header

  1. To create a basic script, you can put the command above into a file called To make it clear what language we expect to use to run the script, we will add the following header on the first line: `#!/bin/bash

    grep ATOM cubane.pdb | wc -l > atoms_cubane.pdb

    The "header" of #!/bin/bash will tell the computer that this is a bash shell script and can be run in the same way that you would run individual commands on the command line. We use /bin/bash instead of just bash because that is the full path to the bash software file. (Run which bash to check!)

    Other languages

    We can use the same principle for any scripting language. For example, the header for a Python script could be either #!/usr/bin/python3 or #!/usr/bin/env python3. Similar logic works for perl, R, julia and other scripting languages.

  2. Can you now run the script?

    $ ./
  3. This gives "permission denied." Let's add executable permissions to the script and try again:

    $ chmod +x
    $ ./

Incorporate Arguments

Can you imagine trying to run this script on all of our pdb files? It would be tedious to edit it for each one, even for only six inputs. Instead, we should add arguments to the script to make it easy to reuse the script. Any information in a script or executable that is going to change or vary across jobs or analyses should likely be turned into an argument that is specified on the command line.

  1. In our example above, which pieces of the script are likely to change or vary?

  2. The name of the input file (cubane.pdb) and output file (atoms_cubane.pdb) should be turned into arguments. Can you envision what our script should look like if we ran it with input arguments?

  3. Let's say we want to be able to run the following command:

    $ ./ cubane.pdb atoms_cubane.pdb

    In order to get arguments from the command line into the script, you have to use special variables in the script. In bash, these are $1 (for the first argument), $2 (for the second argument) and so on. Try to figure out where these should go in our script.

    Other Languages

    Each language is going to have its own syntax for reading command line arguments into the script. In Python, sys.argv is a basic method, and more advanced libraries like argparse can be used. In R, the commandArgs() function can do this. Google "command line arguments in ______" to find the right syntax for your language of choice!

  4. A first pass at adding arguments might look like this:

    grep ATOM $1 | wc -l > $2

    Try running it as described above. Does it work?

  5. While we now have arguments, we have lost some of the readability of our script. The numbers $1 and $2 are not very meaningful in themselves! Let's rewrite the script to assign the arguments to meaningful variable names:

    grep ATOM ${PDB_INPUT} | wc -l > ${PDB_ATOM_OUTPUT}

    Why curly brackets?

    You'll notice above that we started using curly brackets around our variables. While you technically don't need them ($PDB_INPUT would also be fine), using them makes the name of the variable (compared to other text) completely clear. This is especially useful when combining variables with underscores.

  6. There is one final place where we could optimize this script. If we want our output files to always have the same naming convention, based on the input file name, then we shouldn't have a separate argument for that -- it's asking for typos. Instead, we should use variables inside the script to construct the output file name, based on the input file. That will look like this:

    grep ATOM ${PDB_INPUT} | wc -l > ${PDB_ATOM_OUTPUT}

    You may want to construct other variables, like paths and filenames in this way. But it depends on how you want to use the script! If we want the flexibility of specifying a custom output file name, then we should undo this last change so it can be treated as a separate argument.

Your Work

  1. Are you using a scripting language where you could add a header to your main script? If so, what should it be?

  2. What items in your main code or commands are changing? Do you need to add arguments to your code?