Automation, scripts, git, and GitHub

Start up an Ubuntu 14.04 instance and run

sudo bash

apt-get update
apt-get -y install screen git curl gcc make g++ python-dev unzip \
        default-jre pkg-config libncurses5-dev r-base-core \
        r-cran-gplots python-matplotlib sysstat

Automation and scripts

Suppose you want to run a few different commands in succession – this is called “automating tasks”. See

Key caveat: none of the commands require any user input (‘y’, ‘n’, etc)

  1. Figure out what commands you want to run.
  2. Put them in a file using a text editor, like nano or pico, or TextEdit, or TextWrangler, or vi, or emacs.
  3. Run the file.

For example, try putting the following shell commands in a script called ‘’:

cd /root
curl -O
cp Trimmomatic-0.32/trimmomatic-0.32.jar /usr/local/bin
cd /mnt
curl -O
curl -O

java -jar /usr/local/bin/trimmomatic-0.32.jar PE subreads-A-R1.fastq.gz subreads-A-R2.fastq.gz s1_pe s1_se s2_pe s2_se LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25

If you want to do this ghetto style, type:

cd /root
cat >

then paste in the above, put a newline at the end, and then type CTRL-D.

Now, run:


...and this will run all of the stuff that you put in

This is called a shell script (because it is a script for running things, written in shell language). Adina has already told you about Python scripts a bit.

You can do this kind of “scripting” with any set of commands. Just keep track of exactly what you’re teaching at the command line by pasting it into a document somewhere, then save the document in text format, and that’s your script!

Note: what happens when you run ‘bash’ again?

Another note: notice the explicit ‘cd’ steps... why?

But now! You’re stuck keeping track of all of these files.


This is what version control is for.

Here are some things to try.

Some git koans

Forking a repository on github

  1. In a browser, log into

  2. Go to and click “fork” (upper right). This will make a copy of that git repository under your account. It should leave you at<YOUR ACCOUNT>/ngs-scripts.

  3. Select the URL about midway down the page (‘https://...’) and copy it to your clipboard. Hint: There’s a handy little button on the right to do this.

  4. Go to your EC2 command line, and type:

    git clone<YOUR ACCOUNT>/ngs-scripts.git

    where the last bit is pasted from what you copied in step 3.

  5. Change into the ngs-scripts directory:

    cd ngs-scripts/

    and poke around.

  6. Marvel. Note that what is in your directory is the same as what you can see via the github interface.

  7. In a browser, go back to your copy of ngs-scripts. Select ‘’ in the top-level directory.

  8. Select ‘Edit’.

  9. Change something in the text box (e.g. add “Kilroy was here.”)

  10. Click “Commit changes”.

  11. Note that in the browser, has been updated.

  12. In the command line, note that hasn’t changed. The repositories are distinct and separate.

  13. Type:

    git pull<YOUR ACCOUNT>/ngs-scripts.git master

    to pull the changes from github into your local copy.

  14. Now is the same in both places!!

What you have done here is cloned your repository, then edited your file in the original repository, and then pulled the changes from the original repository into your new repository.

Create a new file on github and edit it, then pull

Note the ‘+’ after the directory name (next to ‘branch: ‘) just above the list of files.

This gives you the opportunity to create and edit a new file.

Do so, ‘commit new file’, and then do step #13 above.

Now you’ve created a new file on github!

Edit local file and push to github

At the command line,

  1. Edit the README file (either with a local editor like ‘pico’, or with Dropbox, or something; e.g. do:

    cp ~/Dropbox
    (edit it)
    cp ~/Dropbox/ .

    to update it remotely and copy it back over). Use ‘more’ to make sure your local copy is different.

  2. Type:

    git diff

    to see your changes. The lines with ‘+’ at the beginning are your new changes, the lines with ‘-‘ at the beginning are what they replaced.

  1. Type:

    git commit -am "made some changes"

    to commit the changes as things you want to do.

    (At this point, you could also type ‘git checkout’ to replace the changed file with the original.)

  2. Type:

    git push<YOUR ACCOUNT>/ngs-scripts.git master
  3. Marvel that the local changes are now viewable on directly!

What you have done here is to edit files in one repository, and then pushed the changes to another (remote) repository.

Create a new repository; add some files to it.

Let’s create a new repository, just for you.

In a Web browser,

  1. Go to and click on “New repository.”

  2. Make up a repository name (it will suggest one; ignore it.)

  3. Select the “initialize this repo with a README.”

  4. Select ‘Create repository.”

  5. Now, clone it to your EC2 machine:

    git clone<YOUR ACCOUNT>/<YOUR REPO NAME>.git
  6. Change into the new repo directory:

  7. Create a new file:

    echo hello world > greetings.txt
  8. Add it to your repository:

    git add greetings.txt
  9. Commit it:

    git commit -am "added greetigs"
  10. Push it to your github repository:

    git push<YOUR ACCOUNT>/<YOUR REPO NAME>.git master
  11. Go check it out on the Web – do you see greetings.txt?

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.
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