Bioinformatics Zen


// Sun January 11 2009


Git is a version control system or VCS for short. A VCS helps you manage your code by saving changes as versions in a repository. Each version of any file can be retrieved by rolling back the changes to the required version. At the most basic a VCS allows you the freedom to experiment and actively break the code you're working because the last working version can be reverted to with a single command. Version control is used in software development, and in bioinformatics is useful for keeping track of the scripts and libraries you use in development. Version control using an external server is also a good way to back-up code.


As a VCS git is clean and minimal, working out of a single .git directory in the root of your project. If you want to remove the project from version control, delete the .git directory and all git files are gone. Git managed repositories are small using compression to store the differences between versions. Git is fast at storing the latest version of your code, on even a large repository, it is almost instantaneous. Git repositories are simple to create, and don't necessarily require an external server to begin tracking versions. If you do use an external git server, pushing and pulling to the server is also very fast. Another feature of git allows you to create branches within your code repository. Branching means copying the code as a duplicate branch of the main "master" branch. The duplicate branch can be modified, committed to and then compared with the original branch. If you are happy with the changes in the new branch you can merge them back into the original master branch. Another option is to leave the alternate branch to work on later since switching back to the master branch will restore the previous state before branching. In this way using a branches is a simple and lightweight way to develop or experiment with new features.


Git is useful for collaborating on shared source code repositories. The collaborative development of the Linux kernel is the reason git was created by Linus Torvalds. A key feature of git is that it is distributed. You are not bound by working from a single source server. I have my copy of the repository and you have yours. I like the changes you are making so I clone your repository as a branch into my own. I can test out the changes you've made before merging them into my master branch. If I only want a subset of the changes you've made I can use the git cherry-pick command to merge only the changes I want. The website enables a collaborative aspect of developing software with git. Github acts as a git server but also highlights the social links of branches between developers. Other developers' git repositories can be viewed and downloaded, but also forked into your own github space. This fork acts as a copy of the original repository with the relationship between the two repositories maintained. Github monitors the commits, merges and branching between repositories which can be viewed, compared, or visualised as a network.

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