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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."