Have you ever felt your heart sink upon reading the reviewer comments along the lines of: “very nice analysis, but it would be useful if it was performed on species x, y and z as well”? Or perhaps you have spent weeks analysing data and generating figures only to find out that a newer and more complete data set has become available?

In these circumstances would it not be nice if all you had to do was point your project at a new URL from where the latest version of the data could be downloaded and all the analyses, figures and the manuscript were magically updated for you?

This is possible! In this chapter we will make use of a tool called make to automate all the steps from Data analysis, Data visualisation and Creating scientific documents.

## Introduction to make¶

The make tool is commonly used to build software. As such make is a tool for managing dependencies in a build system, where dependencies are organised into a tree (as in a graph). People in the software industry often talk about dependency graphs.

The make program makes use of a file named Makefile in the working directory. A “Makefile” contains rules. Each rule consists of a target (the stuff to be created), prerequisites (the stuff needed to build the target) and a recipe (the instructions for how to create the target from the prerequisites).

Creating rules in a file named Makefile is therefore a means to create an automated build process.

## Creating a Makefile¶

First of all ensure that you are in the S.coelicolor-local-GC-content directory created in Data analysis.

$cd S.coelicolor-local-GC-content  One of the first steps in Data analysis was to download the S. coelicolor genome. Let’s start by creating a rule for this step. Using your favorite text editor create a file named Makefile and add the content below to it. Sco.dna: curl --location --output Sco.dna http://bit.ly/1Q8eKWT  Warning The make program expects the lines to be indented using the Tab character so make sure that the curl command is preceded by a Tab character and not a bunch of white spaces. In this first rule Sco.dna is the target. The target has no prerequisites and the recipe has one instruction to download the file using curl. Now we can run the make command. $ make
make: Sco.dna' is up to date.


Let’s add another rule for cleaning up the working directory.

Sco.dna:
curl --location --output Sco.dna http://bit.ly/1Q8eKWT

clean:
rm Sco.dna


When invoking make it is possible to specify which rule to run. Let’s clean up.

$make clean rm Sco.dna  If we run make now it will notice that the Sco.dna file does not exist and will download it. $ make
curl --location --output Sco.dna http://bit.ly/1Q8eKWT


Now we need a rule to create the local_gc_content.csv (the target) from the Sco.dna file (the prerequisite). Add the lines below to the top of the Makefile.

local_gc_content.csv: Sco.dna
python dna2csv.py


Now update the clean rule.

clean:
rm Sco.dna
rm local_gc_content.csv


Let’s clean up again.

$make clean rm Sco.dna rm local_gc_content.csv  Now we have removed Sco.dna and local_gc_content.csv. This is a good opportunity to show that make resolves dependencies. We can do this by calling the local_gc_content.csv rule, this will in turn call the Sco.dna rule. $ make local_gc_content.csv
curl --location --output Sco.dna http://bit.ly/1Q8eKWT
python dna2csv.py


That’s cool, make uses the information about requirements to build any missing pieces.

Let’s add another rule for generating the local_gc_content.png file from the local_gc_content.csv file. Add the lines below to the top of the Makefile.

local_gc_content.png: local_gc_content.csv
Rscript csv2png.R


Let’s also remember to update the rule for cleaning up.

clean:
rm Sco.dna
rm local_gc_content.csv
rm local_gc_content.png


Finally, let’s add a rule for building the manuscript as a PDF file and update the clean rule to remove it.

manuscript.pdf: local_gc_content.png
pandoc -f markdown -t latex -s manuscript.md -o manuscript.pdf   \
--filter pandoc-citeproc

local_gc_content.png: local_gc_content.csv
Rscript csv2png.R

local_gc_content.csv: Sco.dna
python dna2csv.py

Sco.dna:
curl --location --output Sco.dna http://bit.ly/1Q8eKWT

clean:
rm Sco.dna
rm local_gc_content.csv
rm local_gc_content.png
rm manuscript.pdf


Let’s try it.

$make clean rm Sco.dna rm local_gc_content.csv rm local_gc_content.png rm manuscript.pdf  Double check that the files have actually been removed. $ ls
Makefile           csv2png.R          nature.csl
bioinformatics.csl manuscript.md


Now let’s build the manuscript.pdf file from scratch.

$make curl --location --output Sco.dna http://bit.ly/1Q8eKWT python dna2csv.py Rscript csv2png.R pandoc -f markdown -t latex -s manuscript.md -o manuscript.pdf \ --filter pandoc-citeproc  Very cool! Now suppose that for some reason we needed to use a different genome file. In this case we would only need to update the URL used in the Makefile’s Sco.dna rule and run make again! Amazing! This is a good point to commit a snapshot of the Git repository. First of all let’s clean up. $ make clean
rm Sco.dna
rm local_gc_content.csv
rm local_gc_content.png
rm manuscript.pdf


Now let’s check the status of the project.

$git status On branch master Your branch is up-to-date with 'origin/master'. Untracked files: (use "git add <file>..." to include in what will be committed) Makefile nothing added to commit but untracked files present (use "git add" to track)  Great let’s add and commit the Makefile. $ git add Makefile
$git commit -m "Added Makefile to build manuscript.pdf" [master 5d74b6a] Added Makefile to build manuscript.pdf 1 file changed, 18 insertions(+) create mode 100644 Makefile  Finally, we push the changes to GitHub. $ git push
Counting objects: 3, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 498 bytes | 0 bytes/s, done.
Total 3 (delta 1), reused 0 (delta 0)
To https://github.com/tjelvar-olsson/S.coelicolor-local-GC-content.git
bea89f4..5d74b6a  master -> master


This was quite a short chapter which illustrates that automation does not need to be painful!

Note that as well as automating the building of the manuscript the rules in the Makefile serve as authoritative documentation that can be used to understand how the different components of the project fit together.

## Key concepts¶

• The make command builds projects using rules specified in the Makefile
• By specifying requirements for each target in the Makefile the make command can work out what the dependency graph is
• It is good practice to specify a clean` rule for removing files that are built automatically