Build Systems
Codebases for scientific projects are usually on the smaller end of the spectrum. They also usually have small development teams. Because they have small teams they have a low bus factor and that cause codebases to fall away quickly when core members move on.
So to solve this problem you could write down a bunch of shell commands used to install or run your code. Or you could just use GNU Make
Intro to Make
See The Art of Bioinformatics Scripting Chapter 2 (Pages 59-73)
Let's commit the changes!
Creating a branch
First, let's learn to make a branch. Here's a visual representation of branches
A branch represents an independent line of development. Branches serve as an abstraction for the edit/stage/commit process. You can think of them as a way to request a brand new working directory, staging area, and project history. New commits are recorded in the history for the current branch, which results in a fork in the history of the project. 3
There are a few ways to create a branch using VS Code. Let's use Ctrl+Shift+P and search for Git: Create Branch from. Then use the name make and then select head or master.
Ctrl+Shift+P- Search for
Git: Create Branch from. - Use
makefor the name of the branch. - Create the branch from
master.
.gitignore
But we have a bunch of build artifacts in our directory. These shouldn't be added to the git repo, because they aren't code(A source of truth), they're something the code creates(A side effect).
You might notice that git picked up all of the txt files. A special file called
.gitignore will tell git to ignore them and avoid tracking their history. Create it and throw the following the file
reads/
refs/
vcf/
*.bam
Commit
Now let's commit it. Same thing as before, refer to The git first commit section if you need a refresher!