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===== GitHub repositories of the lab =====

//By Joran Martijn (Apr 2023)//

GitHub repositories are in its most basic form just //git repositories//, hosted on the internet by the GitHub company. To learn more about the basics of git, checkout the Tips and Tricks slides (and video recording!) [[https://perun.biochem.dal.ca/downloads/icgvideo/TAT/|here]]

==== The RogerLab repositories ====

The Roger lab has an 'organization' account on GitHub, created and currently managed by Joran. If you do not have account yet, create a free GitHub account and ask the current admin to add you. Under this account (click [[https://github.com/RogerLab|here]]), there are currently five repositories:

* gospel_of_andrew
  * fundicalc
  * garp_free_rates
  * gtr_test

These are are private repositories, meaning that only people with GitHub accounts that are members of the RogerLab GitHub organization can access them. They are invisible to the wider world. This is useful if you want to minimize the risk of your projects being scooped, for example.

The [[https://github.com/RogerLab/gospel_of_andrew|gospel_of_andrew]] is simply a collection of various utility scripts that are developed by members of the lab. It's purpose is mainly to serve as a central location where lab members can easily find scripts without having to ask around who has what script. Because it is git-tracked, we can also check past-changes or revert to older versions if newer versions break somehow. There is a README file which has a very brief description of what each script does. 
There is also a directory of ready-baked shell scripts for running softwares on perun. These can serve as templates for your own perun submission scripts.

The other repositories are used for in-development projects of the lab.

When you finish a manuscript and want to submit it to a journal, it is more and more common practice that you publish your code along with it. Your manuscript may for example have a short "Code availability" statement or something along those lines. Creating a public repository under the RogerLab account is an excellent way of doing this. Alternatively, you can create a private repository initially as you are working on your project, and when you are ready to publish, you can change it into a //public// repository.

==== The ICG repositories ====

I've also created a GitHub account for ICG. It isn't used a lot right now, but it may be in the future. These are the [[ https://github.com/orgs/Dalhousie-ICG/repositories|repositories]] currently part of this account.

The [[ https://github.com/Dalhousie-ICG/icg-shared-scripts|icg-shared-scripts ]] serves a similar purpose as the gospel_of_andrew repository, but for anyone within the ICG department.

==== Interacting with the repositories ====

To have access to all the scripts and other files in a repository on your local machine (your laptop, PC, MAC, etc), do the following:

* Open a new Terminal window
  * Go to the directory where you wish to have your local copy of the repository
  * In an internet browser, go to the GitHub website of your desired repository (e.g. https://github.com/RogerLab/gospel_of_andrew). This is the "remote".
  * Click the big "<> Code" button on the top right
  * Copy the displayed URL to your clipboard
  * execute ''git clone <copied_url>'', (e.g. ''git clone git@github.com:RogerLab/gospel_of_andrew.git'')
  * You may be asked to enter your GitHub username and password. If so, do so

The repository should now be downloaded to your local machine!

This means that you in principle don't have to download individual scripts anymore from the GitHub website, you have them all locally available to you. Internet access no longer required :)

In addition, you can now submit changes to the files in the repository and push these changes to the remote. You can also add your own scripts and push them to the remote as well!

==== Saving changes as "commits" ====

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