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 # wphl-bioinformatics
-Bioinformatics scripts for use at the Wyoming Public Health Laboratory
+
+Bioinformatics scripts for use at the Wyoming Public Health Laboratory.
+
+These scripts have various purposes, uses, and instructions. The only unifying thing about them is that they were all written for WPHL. Please check the `README` file in each directory for more detailed instructions.
+
+## Encryption
+
+**NOTICE:** Some files in this repository are encrypted using [git-crypt](https://github.com/AGWA/git-crypt). git-crypt works on a repository-wide basis, meaning that decryption must occur on the entire repository.
+
+### Installing git-crypt
+
+#### Ubuntu, Debian, etc.
+
+```bash
+$ sudo apt-get install git-crypt -y
+```
+
+#### Fedora, CentOS, RHEL, etc.
+
+```bash
+$ sudo yum install git-crypt -y
+```
+
+#### MacOS
+
+Install [Homebrew](https://brew.sh/) first. Then
+
+```bash
+$ brew install git-crypt
+```
+
+#### Windows
+
+There are no official git-crypt builds for Windows. I repeat, **git-crypt does not exist for Windows** regardless of what others may tell you. If possible, you may use the [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10), but you cannot use native git-crypt.
+
+### Decrypting the repository
+
+Encryption is GPG-based. If your GPG key has been added to the repository (you know if you have access), then run
+
+```bash
+$ git clone https://github.com/MillironX/wphl-bioinformatics.git && cd wphl-bioinformatics
+$ git-crypt unlock
+```
+
+The files will now be decrypted and can be usable.
+
+If you need to copy your GPG keys to a new machine to be able to decrypt the files, follow the instructions at https://www.phildev.net/pgp/gpg_moving_keys.html under "Copy Just Your Keys."